Transcript Chapter 14-proteins_part 2

Chapter 14
Proteins
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
a-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
Primary Structure
◦ Vasopressin and oxytocin are both nonapeptides but
have quite different biological functions.
◦ Vasopressin is an antidiuretic hormone.
◦ Oxytocin affects contractions of the uterus in childbirth
and the muscles of the breast that aid in the secretion
of milk.
Figure 22.9 The structures of vasopressin an oxytocin. Differences are
shown in color.
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
a-helix and b-pleated sheet.
◦ a-Helix: A type of secondary structure in which a
section of polypeptide chain coils into a spiral, most
commonly a right-handed 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 a-Helix
Figure 14.10(a)
The a-Helix.
a-Helix
In a section of a-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.
a-Helix

The model is an a-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 N-H 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: a-helix, b-pleated sheet, and random coil
Figure 14.12
Schematic structure
of the enzyme
carboxypeptidase.
The b-pleated sheet
sections are shown
in blue, the a-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 ahelices.
Quaternary Structure
Figure 14.20 An integral
membrane protein from
the outer mitochondrial
membrane forming a bbarrel from eight
b-pleated 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.