Download Chapter 14 Proteins

Chapter 14
Proteins
Proteins
Proteins serve many functions, including the following:
◦ 1. Structure: Collagen and keratin are the chief
constituents of skin, bone, hair, and nails.
◦ 2. Catalysts: Virtually all reactions in living systems are
catalyzed by proteins called enzymes.
◦ 3. Movement: Muscles are made up of proteins called
myosin and actin.
◦ 4. Transport: Hemoglobin transports oxygen from the
lungs to cells; other proteins transport molecules across
cell membranes.
◦ 5. Hormones: Many hormones are proteins, among them
insulin, oxytocin, and human growth hormone.
Proteins
◦ 6. Protection: Blood clotting involves the protein
fibrinogen; the body used proteins called antibodies to
fight disease.
◦ 7. Storage: Casein in milk and ovalbumin in eggs store
nutrients for newborn infants and birds. Ferritin, a protein
in the liver, stores iron.
◦ 8. Regulation: Certain proteins not only control the
expression of genes, but also control when gene expression
takes place.
Proteins

Proteins are divided into two types:
◦ Fibrous proteins: insoluble in water and are used mainly
for structural purposes
◦ long fibers or sheets formed by parallel polypeptide chains
◦ dominated mostly by secondary structure
◦ mostly water insoluble
◦ great strength and/or stretchiness from affects of regular H-bonds
◦ examples:
◦ collagen in connective tissue
◦ actin and myosin in muscle tissue
Proteins

Globular proteins: more or less soluble in water and are
used for nonstructural purpose
◦ folded into complex 3-D irregular spherical shape
◦ dominated mostly by tertiary structure
◦ mostly water soluble
◦ functions determined by 3-D shape
◦ examples:
◦ enzymes such as amylase
◦ hormones such as insulin
◦ transport such as hemoglobin
◦ protective, such as immunoglobulins
Amino Acids
Amino acid: A compound that contains both an amino
group and a carboxyl group.
◦ -Amino acid: An amino acid in which the amino group
is on the carbon adjacent to the carboxyl group.
Table 14.1 The 20 amino acids commonly found in proteins
Chirality of -Amino Acids
With the exception of glycine, all protein-derived amino acids
have at least one stereocenter (the -carbon) and are chiral.
◦ The vast majority of -amino acids have the L-configuration
at the -carbon.
Chirality of -Amino Acids
A comparison of the configuration of L-alanine and Dglyceraldehyde (as Fischer projections):
Protein-Derived -Amino Acids
Nonpolar side chains. Each ionizable group is shown in the
form present in highest concentration at pH 7.0).
Protein-Derived -Amino Acids

Polar side chains (at pH 7.0)
Protein-Derived -Amino Acids
Acidic and basic side chains (at pH 7.0)
Protein-Derived -Amino Acids
1. For 19 of the 20, the -amino group is primary; for proline,
it is secondary.
2. With the exception of glycine, the -carbon of each is a
stereocenter.
3. Isoleucine (left) and threonine (right) contain a second
stereocenter.
Ionization vs. pH
The net charge on an amino acid depends on the pH of the
solution in which it is dissolved.
◦ If we dissolve an amino acid in water, it is present in the
aqueous solution as its zwitterion.
Ionization vs. pH

To summarize
:
pH = 0
a zwitterion
pH = 7
pH = ~ 14
Isoelectric Point (pI)

Isoelectric point, pI:
The pH at which
the majority of
molecules of a
compound in
solution have no
net charge.
Nonpolar &
polar side chains
alanine
asparagine
cysteine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tyrosine
tryptophan
valine
pI
6.01
5.41
5.07
5.65
5.97
6.02
5.98
5.74
5.48
6.48
5.68
5.87
5.66
5.88
5.97
Acidic
pI
Side Chains
aspartic acid 2.77
glutamic acid 3.22
Basic
pI
Side Chains
10.76
arginine
histidine
7.59
lysine
9.74
What determines the characteristic of
amino acid
Cystine
The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S(disulfide).
Hair is made up by a protein called karetin that contains a large number
of cysteine residues
Peptides
In 1902, Emil Fischer proposed that proteins are long chains of
amino acids joined by amide bonds.
◦ Peptide bond (peptide linkage): The special name given to the
amide bond between the -carboxyl group of one amino acid
and the -amino group of another.
Peptides
◦ Peptide: A short polymer of amino acids joined by peptide
bonds; they are classified by the number of amino acids in
the chain.
◦ Dipeptide: A molecule containing two amino acids joined by
a peptide bond.
◦ Tripeptide: A molecule containing three amino acids joined
by peptide bonds.
◦ Polypeptide: A macromolecule containing many amino acids
joined by peptide bonds.
◦ Protein: A biological macromolecule containing at least 30 to
50 amino acids joined by peptide bonds.
◦ The individual amino acid units are often referred to as
“residues”.
Peptide Bond

A peptide bond is typically written as a carbonyl group bonded to
an N-H group. Linus Pauling, however, discovered that there is
about 40% double bond character to the C-N bond and that a
peptide bond between two amino acids is planar, which Pauling
explained using the concept of resonance.
Peptide bond
Writing Peptides
By convention, peptides are written from the left to right,
beginning with the free -NH3+ group and ending with the free COO- group.
◦ C-terminal amino acid: The amino acid at the end of the chain
having the free -COO- group.
◦ N-terminal amino acid: The amino acid at the end of the chain
having the free -NH3+ group.
Writing Peptide Bond
Example

Show how to form the dipeptide Gly-Val

Draw the tetrapeptide Ala-Thr-Asp-Asn and indicate the
peptide bond
Peptides and Proteins
Proteins behave as zwitterions.
Proteins also have an isoelectric point, pI.
◦ At its isoelectric point, the protein has no net charge.
◦ At any pH above (more basic than) its pI, it has a net negative
charge.
◦ At any pH below (more acidic than) its pI, it has a net positive
charge.
◦ Hemoglobin, for example, has an almost equal number of acidic
and basic side chains; its pI is 6.8.
◦ Serum albumin has more acidic side chains; its pI is 4.9.
◦ Proteins are least soluble in water at their isoelectric points and
can be precipitated from solution
at this pH.
Levels of Structure

Primary structure: The sequence of amino acids in a
polypeptide chain. Read from the N-terminal amino acid to the
C-terminal amino acid.

Secondary structure: Conformations of amino acids in localized
regions of a polypeptide chain. Examples are
-helix, b-pleated sheet, and random coil.

Tertiary structure: The complete three-dimensional
arrangement of atoms of a polypeptide chain.

Quaternary structure: The spatial relationship and interactions
between subunits in a protein that has more than one
polypeptide chain.
Primary Structure
Primary structure: The sequence of amino acids in a polypeptide
chain.
The number peptides possible from the 20 protein-derived amino
acids is enormous.
◦ There are 20 x 20 = 400 dipeptides possible.
◦ There are 20 x 20 x 20 = 8000 tripeptides possible.
◦ The number of peptides possible for a chain of n amino acids is
20n.
◦ For a small protein of 60 amino acids, the number of proteins
possible is 2060 = 1078, which is possibly greater than the number
of atoms in the universe!
Primary Structure
Figure 14.8 The
hormone insulin
consists of two
polypeptide chains, A
and B, held together by
two disulfide bonds.
The sequence shown
here is for bovine
insulin.
Primary Structure
How important is the exact amino acid sequence?
◦ Human insulin consists of two polypeptide chains having a total
of 51 amino acids; the two chains are connected by two interchain
disulfide bonds.
◦ In the table are differences between four types of insulin.
A Chain
positions 8-9-10
B Chain
position 30
Human
Cow
-Thr-Ser-Ile-Ala-Ser-Val-
-Thr
-Ala
Hog
Sheep
-Thr-Ser-Ile-Ala-Gly-Val-
-Ala
-Ala
Secondary Structure
Secondary structure: describes the repetitive conformation
assumed by the segment of the backbone of a peptide or protein
◦ The most common types of secondary structure are
-helix and b-pleated sheet.
◦ -Helix: A type of secondary structure in which a section of
polypeptide chain coils into a spiral, most commonly a righthanded spiral.
◦ b-Pleated sheet: A type of secondary structure in which two
polypeptide chains or sections of the same polypeptide chain
align parallel to each other; the chains may be parallel or
antiparallel.
Secondary Structure: The -Helix
Figure 14.10(a) The
-Helix.
-Helix
In a section of -helix
◦ There are 3.6 amino acids per turn of the helix.
◦ The six atoms of each peptide bond lie in the same plane.
◦ The N-H groups of peptide bonds point in the same direction,
roughly parallel to the axis of the helix.
◦ The C=O groups of peptide bonds point in the opposite
direction, also roughly parallel to the axis of the helix.
◦ The C=O group of each peptide bond is hydrogen bonded to the
N-H group of the peptide bond four amino acid units away from
it.
◦ All R- groups point outward from the helix.
-Helix

The model is an -helix section of polyalanine, a polypeptide
derived entirely from alanine. The intrachain hydrogen bonds
that stabilize the helix are visible as the interacting C=O and NH bonds.
b-Pleated Sheet
Figure 14.10(b) The
b-pleated sheet
structure.
b-Pleated sheet
In a section of b-pleated sheet;
◦ The polypeptide backbone is extended in a zigzag structure
resembling a series of pleats.
◦ The six atoms of each peptide bond of a b-pleated sheet lie in
the same plane.
◦ The C=O and N-H groups of the peptide bonds from adjacent
chains point toward each other and are in the same plane so that
hydrogen bonding is possible between them.
◦ All R- groups on any one chain alternate, first above, then below
the plane of the sheet, etc.
β-Pleated Sheet
Secondary Structure

Many globular proteins contain all three kinds of secondary
structure in different parts of their molecules: -helix, bpleated sheet, and random coil
Figure 14.12
Schematic structure
of the enzyme
carboxypeptidase.
The b-pleated sheet
sections are shown
in blue, the -helix
portions in green,
and the random
coils as orange
strings.
Random Coil
Figure 14.11
The rest of the molecule
is a random coil.
Tertiary Structure
Tertiary structure: the overall conformation of an entire
polypeptide chain.
Tertiary structure is stabilized in four ways:
◦ Covalent bonds, as for example, the formation of disulfide
bonds between cysteine side chains.
◦ Hydrogen bonding between polar groups of side chains, as
for example between the -OH groups of serine and
threonine.
◦ Salt bridges, as for example, the attraction of the -NH3+ group
of lysine and the -COO- group of aspartic acid.
◦ Hydrophobic interactions, as for example, between the
nonpolar side chains of phenylalanine and isoleucine.
The Collagen Triple Helix
Figure 14.13 The collagen
triple helix.
Non covalent interactions that stabilize the tertiary and quaternary structures
of protein: a) Hydrogen bonding, b) salt bridge, c) hydrophobic interaction,
and d) Metal ion coordination
Tertiary Structure
Figure 14.20 Forces that stabilize tertiary structures of proteins.
Quaternary Structure
Quaternary structure: The threee-dimension arrangement
of every atom in the molecule.
◦ The individual chains are held together by hydrogen
bonds, salt bridges, and hydrophobic interactions.
Hemoglobin
◦ Adult hemoglobin: Two alpha chains of 141 amino acids
each, and two beta chains of 146 amino acids each.
◦ Fetal hemoglobin: Two alpha chains and two gamma
chains. Fetal hemoglobin has a greater affinity for oxygen
than does adult hemoglobin.
◦ Each chain surrounds an iron-containing heme unit.
Quaternary Structure
Figure 14.22 The quaternary structure of hemoglobin. The
structure of heme is shown on the next screen.
Quaternary Structure
Figure 14.18 The structure of heme
Quaternary Structure
Integral membrane proteins form quaternary structures in
which the outer surface is largely nonpolar (hydrophobic) and
interacts with the lipid bilayer. Two of these are shown on the
next screens.
Figure 14.19 Integral
membrane protein of
rhodopsin, made of helices.
Quaternary Structure
Figure 14.20 An integral
membrane protein from the
outer mitochondrial
membrane forming a bbarrel from eight
bpleated sheets.
Denaturation
Denaturation: The process of destroying the native
conformation of a protein by chemical or physical means.
◦ Some denaturations are reversible, while others permanently
damage the protein.
Denaturing agents include:
◦ Heat: heat can disrupt hydrogen bonding; in globular
proteins, it can cause unfolding of polypeptide chains with
the result that coagulation and precipitation may take place.
Denaturation
◦ 6 M aqueous urea: Disrupts hydrogen bonding.
◦ Surface-active agents: Detergents such as sodium
dodecylbenzenesulfate (SDS) disrupt hydrogen bonding.
◦ Reducing agents: 2-Mercaptoethanol (HOCH2CH2SH)
cleaves disulfide bonds by reducing -S-S- groups to -SH
groups.
◦ Heavy metal ions: Transition metal ions such as Pb2+, Hg2+,
and Cd2+ form water-insoluble salts with -SH groups; Hg2+
for example forms -S-Hg-S-.
◦ Alcohols: 70% ethanol penetrates bacteria and kills them by
coagulating their proteins. It is used to sterilize skin before
injections.