Download Chapter 22, Proteins

Chemistry 110
Bettelheim, Brown, Campbell & Farrell
Ninth Edition
Introduction to General,
Organic and Biochemistry
Chapter 22
Proteins
Step-growth polyamide (polypeptide) polymers or oligomers
of L-α-aminoacids.
Proteins have Many Functions
¾Structure: collagen and keratin are the chief constituents of skin,
bone, hair, and nails.
¾Catalysts: virtually all reactions in living systems are catalyzed by
proteins called enzymes.
¾Movement: muscles are made up of proteins called myosin and
actin.
¾Transport:
Transport hemoglobin transports oxygen from the lungs to cells;
other proteins transport molecules across cell membranes.
¾Hormones: many hormones are proteins, among them insulin,
oxytocin, and human growth hormone.
¾Protection: the body used proteins called antibodies to fight
disease; blood clotting involves the protein fibrinogen.
¾Storage: casein in milk and ovalbumin in eggs store nutrients for
infants and birds; ferritin, a protein in the liver, stores iron.
¾Regulation: specific proteins control the expression of genes, others
control when gene expression takes place.
Peptides & Proteins
¾Emil Fischer proposed in 1902 that proteins are long chains of
amino acids joined by amide bonds. The special name given to
the amide bond between the α-carboxyl group of one amino acid
and the α-amino group of another is called a peptide bond.
¾A short polymer of amino acids joined by peptide bonds are
classified by the number of amino acids in the chain.
¾A dipeptide is a molecule containing two amino acids joined by
a peptide bond.
¾A tripeptide is a molecule containing three amino acids joined
by two peptide bonds.
¾A polypeptide is a macromolecule containing many amino
acids joined by peptide bonds.
¾A protein is defined as a biological macromolecule containing
at least 30 to 50 amino acids joined by peptide bonds.
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Proteins and Amino Acids
¾Proteins are step-growth polymers of alpha aminoacids.
¾Proteins are of two types, fibrous and globular.
¾Amino acid are compound that contains both an amino group
and a carboxyl group. In α--amino acids the amino group is on
the carbon adjacent to the carboxyl group.
¾Although α-amino acids are commonly written in the unionized form, they are more properly written in the zwitterion
(internal salt) form.
¾With the exception of glycine, all protein-derived amino acids
have at least one stereocenter (the α-carbon) and are chiral.
¾Two α−aminoacids, threonine and isoleucine, have a second
stereocenter.
¾The vast majority of α-amino acids have the L-configuration
at the α-carbon.
Proteins - Polymers of Alpha Aminoacids
When a pure aminoacid
is dissolved in water it
has this form.
The pH will be a value
called the pI.
OH
H
O
NH3 CH COH
R
acidic solution
pH < 2.0
This is the isoelectric
form. The molecule
has no net charge.
O
NH3 CH CO
A “zwitterion” or
internal salt.
OH
R
H
O
Aminoacids are NH2 CH CO
ionic at all pH
R
values and remain
soluble in aqueous basic solution
pH > 10
solution.
In strong Acid the aminoacid
will be a cation, net positive.
In strong base the aminoacid
will be an anion, net negative.
The “Standard Set” of Amino Acids
O
NH3 CH CO
Always shown at the isoelectric point
The "non-polar" side chain group: R =
H
6.06
Glycine
Gly G
CH3
CH3
CH
6.11
Alanine
Ala A
CH3
6.00
Valine
Val V
R
CH3
CH2CH
CH3
6.04
Leucine
Leu L
CH2
H2C
5.91
Phenylalanine
Phe F
CH2CH2SCH3
N
H 5.88
Tryptophan
Trp W
5.74
Methionine
Met M
CHCH2CH3
CH3
6.04
Isoleucine
Ile I
O
O C
H N
H
6.30
Proline
Pro P
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The “Standard Set” of Amino Acids
O
NH3 CH CO
Always shown at the isoelectric point
R
The side chain has a polar, but neutral, group: R =
H
CH2OH
COH
O
CH2CNH2
O
CH2CH2CNH2
5.68
Serine
Ser S
CH3
5.64
Threonine
Thr T
5.41
Asparagine
Asn N
5.65
Glutamine
Gln Q
¾These groups will orient in a protein so that they project toward
the aqueous layer, and will not associate with nonpolar groups.
¾They can form hydrogen bonds with water and with each other.
The “Standard Set” of Amino Acids
O
NH3 CH CO
Always shown at the isoelectric point
The side chain is acidic: R =
O
CH2COH
R
O
CH2CH2COH H2C
2.98
3.08
Aspartic Acid Glutamic Acid
Glu E
Asp D
The side chain is basic: R =
OH
5.63
Tyrosine
Tyr Y
NH
CH2CH2CH2CH2NH2 CH2CH2CH2NHCNH2
9.47
Lysine
Lys K
10.76
Arginine
Arg R
CH2SH
5.07
Cysteine
Cys C
H2C
N
H
N
7.64
Histidine
His H
Protein Behavior & Levels of Structure
¾Proteins behave as zwitterions and have an isoelectric point, pI,
pI,
because their side groups can be acidic and basic. Hemoglobin
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.
¾Proteins are least soluble in water at their isoelectric points and
can be precipitated from their solutions.
¾The primary structure is the sequence of amino acids in a
polypeptide chain; read from the N-terminal amino acid to the Cterminal amino acid.
¾The secondary
econdary structure is the conformations of amino acids in
localized regions of a polypeptide chain; examples are α-helix, βpleated sheet, and random coil.
¾The tertiary structure is the overall conformation of a
polypeptide chain.
¾A quaternary
uaternary structure is the arrangement of two or more
polypeptide chains into a non-covalently bonded aggregation.
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The “Primary Structure” of Proteins
H
O
H N CH C O
H R'
H
O
H N CH C O
H R
H
O
H N CH C O
H R"
H2O
H2O
O
O
O
C N CH C N CH C O
H R'
H R"
H
H N CH
H R
N-terminal residue
C-terminal residue
Peptide Bonds
¾The primary structure of proteins is the specific sequence of
aminoacids in the protein chain.
¾Proteins are always written with the N-terminus on the left.
Secondary Structure of Proteins
H
H N CH
H
R
H
H N CH
H
R
O
C
N CH
H
O
C
R'
N CH
H
R'
O
C
N CH
H
O
C
O
R"
N CH
H
O
C
O
C
O
R"
¾Hydrogen Bonds can form between adjacent strands of
polypeptide or with different portions of the same strand.
¾A stable alpha-helix has the hydrogen bonds forming between
each peptide residue and the fourth peptide removed. In
structural proteins a left-handed helix may form.
¾A beta-pleated sheet has the hydrogen bonds between adjacent
segments.
The Alpha Helix
¾In a section of α-helix there are 3.6 amino acids per turn of
the helix.
¾The six atoms of each peptide bond lie in the same plane.
¾The N-H groups of peptide bonds point in the same direction,
roughly parallel to the axis of the helix.
¾The C=O groups of peptide bonds point in the direction
opposite the N-H groups, also roughly parallel to the axis of the
helix.
¾The 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.
¾All the R- groups of the aminoacids point outward from the
helix
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The Beta Pleated Sheet
¾In a section of β-pleated sheet the six atoms of each peptide
bond lie in the same plane.
¾The C=O and N-H groups of peptide bonds from adjacent
chains point toward each other and are in the same plane so that
hydrogen bonding is possible between them.
¾All R-groups on any one chain alternate, first above, then
below the plane of the sheet, etc.
¾The distinction between secondary structure (α-helix, β-pleated
sheets) and tertiary structure is that secondary structures are
stabilized only by hydrogen bonds arising through the peptide
units, while tertiary structure may utilize more varied elements.
¾Usually only certain portions of protein molecules, especially
globular proteins, are α-helix or β-pleated sheets. The
remainder is commonly random coil.
¾Some proteins, e.g. keratin, are predominately α-helix.
The Collagen Triplehelix
¾Collagen consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix called
tropocollagen.
¾30% of amino acids in each chain are proline and Lhydroxyproline (Hyp); L-hydroxylysine (Hyl) also occurs.
¾Every third position is glycine and repeating sequences are XPro-Gly and X-Hyp-Gly.
¾Each polypeptide chain is a helix, called an extended helix,
but not an α-helix.
¾The three strands are held together by hydrogen bonding
involving hydroxyproline and hydroxylysine.
¾With age, the collagen helices become cross linked by covalent
bonds formed between lysine residues. This is a factor in aging,
muscle stiffness, etc.
Tertiary Structure of Proteins
¾The tertiary structure of a protein is the overall conformation
of a polypeptide chain caused by side-group interaction.
¾The side-groups of proteins project outward from either the
helices or the sheets. Side-groups in contact with the aqueous
medium tend to cause folding of the helical strands or sheets.
¾Hydrophobic side-chains aggregate to minimize contact with
water. They tend to tuck inside away from water.
¾Hydrophilic side-groups extend themselves in order to
hydrogen-bond with the aqueous medium.
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Tertiary Structure of Proteins
The tertiary structure of a protein is stabilized in four ways:
¾Covalent bonds, most commonly the formation of disulfide
bonds between cysteine side chains.
COO
2 HSCH2 C H
[O]
COO
H C CH2S
COO
SCH2 C H
NH3
NH3
NH3
¾Hydrogen bonding between polar groups of side chains, such as
between the -OH groups of serine and threonine.
¾Salt bridges,
bridges formation of ionic bonds, most commonly the
attraction of the side group ammonium ions of one of the basic
aminoacids, (lysine, arginine) and the -COO- in the side-group of
one of the acidic aminoacids (aspartic acid, glutamic acid).
¾Hydrophobic
ydrophobic interactions,
interactions such as between the nonpolar side
chains of phenylalanine, leucine, isoleucine.
Quaternary Structures of Proteins
¾The quaternary structure is the arrangement of polypeptide
chains into a noncovalently bonded aggregation.
¾The individual chains are held in together by hydrogen
bonds, salt bridges, and hydrophobic interactions.
¾Prosthetic Groups often get incorporated.
1) In one case, collagen, three helical coils form a triple
helix, like a steel cable. Although the lysine side chain
residues are linked together by covalent bonds, the
triple strands of tropocollagen eventually overlap
lengthwise to form fibrils or micro-fibres.
2) In another case, adult hemoglobin, two alpha chains of
141 amino acids each, and two beta chains of 146 amino
acids each combine with each chain surrounding an
iron-containing heme prosthetic group unit. Fetal
etal
hemoglobin is slightly different.
Glycoproteins
¾A glycoprotein is a protein to which one or more carbohydrate
units are bonded. There are two common types:
¾OxygenOxygen-linked saccharides in which a glycosidic bond between
the anomeric carbon of a saccharide and the OH group of
serine, threonine, or hydroxylysine has been formed. Example:
the mucins which coat and protect mucous membranes.
¾NitrogenNitrogen-linked saccharides in which an N-glycosidic bond
between the anomeric carbon of N-acetyl-D-glucosamine and the
nitrogen of the side chain amide group of asparagine has been
formed. Examples are the proteoglycans.
HO
H2COH
HO
HN
O
HO
C O
O CH2 C H HO
NH
O C
CH3
H2COH
HN
O
O
C O
N C CH2 C H
H
NH
O C
β-N-Acetyl-D-glucosyl-serine
CH3
β-N-Acetyl-D-glucosyl-asparagine
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Denaturation
Denaturation is the process of destroying the native shape or
conformation of a protein by chemical or physical means. Some
denaturations are reversible, while others permanently damage
the protein.
Methods involve both physical and chemical means.
Few methods change the primary structure of proteins.
Physical denaturing agents include:
¾Heat can disrupt hydrogen bonding; in globular proteins
unfolding of the polypeptide chains may occur resulting in
coagulation and precipitation.
¾Sonic disruption or whipping can disrupt tertiary and
quaternary structure.
¾Dehydration – removal of water, drying-out can change
tertiary and quaternary structure.
Denaturation
Chemical denaturing agents include:
¾6 M aqueous urea will disrupt hydrogen bonding.
¾SurfaceSurface-active agents such as detergents disrupt hydrogen
bonding.
¾Reducing agents commonly 2-mercaptoethanol
(HOCH2CH2SH) cleaves disulfide bonds by reducing -S-Sgroups to -SH groups. Permanent wave processes do this.
¾Heavy metal ions such as:
as Pb2+, Hg2+, and Cd2+ form waterinsoluble salts with -SH groups on cysteine. Hg2+ for example
forms -S-Hg-S-.
¾Alcohols affect the water content and hydrophobic/hydrophilic
relationships. 70% ethanol, for example, which denatures
proteins, is used to sterilize skin before injections
Digestion of Proteins
Hydrolysis (breakdown) Recovers Constituent Amino Acids.
Peptide Bonds
H
O
O
O
H N CH C N CH C N CH C O
H R
H R'
H R"
+ H2 O
+ H2O
H
O
H N CH C O
H R
H
O
H N CH C O
H R'
H
O
H N CH C O
H R"
Essential aminoacids, ones our bodies cannot make, are obtained
this way from our diet. All the others can be obtained too.
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Common Properties of Proteins
¾Protein shape is essential to its function. Sometimes changing
its shape can be lethal – Prions – Proteinaceous Infectuous
Particles – are altered proteins that can cause natural proteins to
change shape – Mad Cow disease or Bovine Spongiform
Encephalopathy, Scrapie, Kuru, Creutzfeldt-Jacob disease.
¾Sometimes a single aminoacid substitution can cause a protein
to have the wrong shape. Sickle cell anemia is an example.
¾Proteins have isoelectric points just like amino acids. At the
isoelectric points proteins are uncharged (net neutral, dipolar)
and clump together (precipitate, denature). Away from the
isoelectric point they have a like charge, either positive or
negative and repel each other thus remaining in solution.
¾At the isoelectric point neither proteins nor amino acids will
drift toward either electrode (anode or cathode) in an electric
field.
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