Biochemistry Proteins Midterm

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Bioche

Proteins
m:
Proteins
- are biological polymers composed of amino acids.

Amino acids, linked together by peptide bonds, form a polypeptide chain.

One or more polypeptide chains twisted into a 3-D shape form a protein.

Proteins serve many functions, including the following:

1. Structure: Collagen and keratin are the chief constituents of skin, bone, hair, and nails.
2. Catalysis: 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.
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 are divided into two types:


 Fibrous proteins
 Globular proteins

Amino Acids

Amino acid: A compound that contains both an amino group and a carboxyl group.

α-Amino acid: An amino acid in which the amino group is on the carbon adjacent to the
carboxyl group.

Although α-amino acids are commonly written in the un-ionized form, they are more properly
written in the zwitterion (internal salt) form.

Chirality of α-Amino Acids (1 of 2)

With the exception of glycine, all protein-derived amino acids have at least one stereocenter
(the α-carbon) and are chiral.
• The vast majority of α-amino acids have the L-configuration at the α-carbon.
Chirality of α-Amino Acids (2 of 2)

Figure 21.2 Alanine and glyceraldehyde stereochemistry

Protein-Derived α-Amino Acids (1 of 4)

Nonpolar side chains. Each ionizable group is shown in the form present in highest
concentration at pH 7.0).

Protein-Derived α-Amino Acids (2 of 4)

• Polar side chains (at pH 7.0)

Protein-Derived α-Amino Acids (3 of 4)

 Acidic and basic side chains (at pH 7.0)


Protein-Derived α-Amino Acids (4 of 4)
1. For 19 of the 20, the α-amino group is primary; for proline, it is secondary.
2. With the exception of glycine, the α-carbon of each is a stereocenter.
3. Isoleucine (left) and threonine (right) contain a second stereocenter.

Ionization vs. pH (1 of 2)

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.
• If we add a strong acid such as HCl to bring the pH of the solution to pH 0, the
strong acid donates a proton to the –COO– of the zwitterion turning it into a
positive ion.

Ionization vs. pH (2 of 2)

• If we add a strong base such as NaOH to the solution and bring its pH to 14, a
proton is transferred from the NH3+ group to the base turning the zwitterion into
a negative ion.

• To summariz

Protein Properties (2 of 2)

Proteins behave as zwitterions.


Proteins 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 when pH = pI.
Isoelectric Point (pI)

• Isoelectric point, pI:


A pH at which a sample of amino acids or
protein has an equal number of positive and negative
charges.

Note:
Acidic side chains: the pI is lower
Basic side chains: the pI is higher
Nonpolar&polar side chains: the pI is moderate

Peptides (1 of 2)

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 α-carboxyl group of one amino acid and the α-amino group of
another.

Peptides (2 of 2)

• 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.”

Writing Peptides

By convention, peptides are written from the left to right, beginning with the free –NH 3+ 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.
• Alternatively they are referred to as the C-terminus and the N-terminus.

Phe, Trp, and Tyr

The amino acids phenylalanine, tryptophan, and tyrosine have aromatic rings on their
side chains.
Tryptophan is the precursor to the neurotransmitter serotonin.
Tyr and Phe

Phenylalanine and tyrosine are precursors to norepinephrine and epinephrine, both of


which are stimulatory neurotransmitters.

Other Amino Acids

Figure 21.3 Hydroxylation (oxidation) of proline, lysine, and tyrosine,


respectively and iodination for tyrosine, give these uncommon amino
acids.

Protein Properties (1 of 2)

Figure 21.4 A small peptide showing the direction of the peptide chain
(N-terminal to C-terminal).

Peptide Bond

• Figure 21.5. 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.

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
α-helix, β-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 × 20 = 400 dipeptides possible.
• There are 20 × 20 × 20 = 8000 tripetides 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!

Figure 21.7 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.

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 Table 21.2 are differences between four types of insulin.

A Chain B Chain
positions 8-9- position 30
10
Human -Thr-Ser-Ile -Thr
Cow -Ala-Ser-Val- -Ala
Hog -Thr-Ser-Ile- -Ala
Sheep -Ala-Gly-Val- -Ala

 Vasopressin and oxytocin are both Nona peptides 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 21.8 The structures of vasopressin and oxytocin.


Differences are shown in color.

Secondary Structure

Secondary structure: Conformations of amino acids in localized regions of a polypeptide


chain.
• The most common types of secondary structure are
α-helix and β-pleated sheet.
• α-Helix: A type of secondary structure in which a section of polypeptide chain
coils into a spiral, most commonly a right-handed spiral.
• β-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.
Figure 21.9(a) The α-Helix.

In a section of α-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.

Figure 21.9(b) The β-pleated sheet structure.

In a section of β-pleated sheet;


• The six atoms of each peptide bond of a
β-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.

Random Coil

Figure 21.10 A random coil.

Many globular proteins contain all three kinds of secondary structure in different parts of their
molecules: α-helix, β-pleated sheet, and random coil.

Figure 21.11 Schematic structure of the enzyme carboxypeptidase. The β-pleated sheet
sections are shown in blue, the α-helix portions in green, and the random coils as orange
strings.
The Collagen Triple Helix

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 –NH 3+ group of lysine and
the –COO– group of aspartic acid.
• Hydrophobic interactions, as for example, between the nonpolar side chains
of phenylalanine and isoleucine.

Cysteine

The –SH (sulfhydryl) group of cysteine is easily oxidized to an –S–S– (disulfide).

Figure 21.14 Forces that stabilize tertiary structures of proteins.

Quaternary Structure

Quaternary structure: The arrangement of polypeptide chains into a noncovalently


bonded aggregation.
• 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.
Figure 21.20 The quaternary structure of hemoglobin. The structure of heme is
shown.

The structure of heme.

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.
• 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.

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