Biochemistry Proteins Midterm
Biochemistry Proteins Midterm
Biochemistry Proteins Midterm
Proteins
m:
Proteins
- are biological polymers composed of amino acids.
One or more polypeptide chains twisted into a 3-D shape form a protein.
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.
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.
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)
Nonpolar side chains. Each ionizable group is shown in the form present in highest
concentration at pH 7.0).
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)
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)
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.
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
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
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:
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
Secondary Structure
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.
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
Cysteine
Quaternary Structure
Denaturation