Bio Chemistry - Proteins

Proteins

are long chains of amino acids joined by amide bonds

Structure

Collagen and keratin are the chief constituents of skin, bone, hair, and nails.

Catalysis

Virtually all reactions in living systems are catalyzed by proteins called enzymes.

Movement

Muscles are made up of proteins called myosin and actin.

Transport

Hemoglobin transports oxygen from the lungs to cells, other proteins transport molecules across cell membranes.

Hormones

Many hormones are proteins, among them insulin, oxytocin, and human growth hormone.

Protection

Blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease.

Storage

Casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds. Ferritin, a protein in the liver, stores iron.

Regulation

Certain proteins not only control the expression of genes, but also control when gene expression takes place.

Fibrous proteins • Globular proteins

Proteins are divided into two types:

Amino acid

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

a-Amino acid

An amino acid in which the amino group is on the carbon adjacent to the carboxyl group.

zwitterion (internal salt) form.

Although a-amino acids are commonly written in the un-ionized form, they are more properly written in the __________________ .

Isoelectric point, pI

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

Peptide bond (peptide linkage)

The special name given to the amide bond between the a-carboxyl group of one amino acid and the a-amino group of another.

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.

residues

The individual amino acid units are often referred to as…

left to right

peptides are written from

free –NH3 + group

peptides are written, beginning with the

free –COO– group.

peptides are written, ending with the

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.

C-terminus and the Nterminus.

Alternative terms for C-Terminal amino acid & N-Terminal amino acid

phenylalanine, tryptophan, and tyrosine

amino acids which have aromatic rings on their side chains:

Tryptophan

the precursor to the neurotransmitter serotonin

Phenylalanine and tyrosine

are precursors to norepinephrine and epinephrine, both of which are stimulatory neurotransmitters.

peptide bond

__________ is typically written as a carbonyl group bonded to an N–H group

Linus Pauling,

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, w

the protein has no net charge.

At its isoelectric point,

it has a net negative charge.

At any pH above (more basic than) its pI

it has a net positive charge.

At any pH below (more acidic than) its pI,

least soluble

Proteins are ___________ in water at their isoelectric points

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.

20n.

The number of peptides possible for a chain of n amino acids is

A and B

The hormone insulin consists of two polypeptide chains

two disulfide bonds.

This holds the two polypeptide chains [a and b] in the hormone insulin:

Human insulin

consists of two polypeptide chains having a total of 51 amino acids;

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.

a-helix and b-pleated sheet.

The most common types of secondary structure are

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.

six

In a section of a-helix, The ____ atoms of each peptide bond lie in the same plane.

same direction, roughly parallel to the axis of the helix.

The N–H groups of peptide bonds point in the

opposite direction, also roughly parallel to the axis of the helix

The C=O groups of peptide bonds point in the

outward

All R– groups point _______ from the helix.

six

In a section of b-pleated sheet, The ______ atoms of each peptide bond of a b-pleated sheet lie in the same plane.

toward each other and are in the same plane so that hydrogen bonding is possible between them.

The C=O and N–H groups of the peptide bonds from adjacent chains point

one chain, alternate first above, then below the plane of the sheet, etc

All R– groups on any ______

a-helix, b-pleated sheet, and random coil.

Many globular proteins contain all three kinds of secondary structure in different parts of their molecules:

Ionic bonds, Hydrogen bonding, Salt bridges, Hydrophobic interactions,

Tertiary structure is stabilized in four ways:

S–S– (disulfide).

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

Quaternary structure

The arrangement of polypeptide chains into a noncovalently bonded aggregation.

hydrogen bonds, salt bridges, and hydrophobic interactions.

individual chains found in quaternary structures are held together by

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.

iron-containing heme unit.

Each chain surrounds an

Denaturation

The process of destroying the native conformation of a protein by chemical or physical means.

reversible, while others permanently damage the protein

Some denaturations are

Heat

Denaturing agents include: Heat can disrupt hydrogen bonding

6 M aqueous urea

Denaturing agents include: Disrupts hydrogen bonding.

Surface-active agents

Denaturing agents include: Detergents such as sodium dodecylbenzenesulfate (SDS) disrupt hydrogen bonding.

Reducing agents

Denaturing agents include: 2-Mercaptoethanol (HOCH2CH2SH) cleaves disulfide bonds by reducing –S–S– groups to –SH groups.

Heavy metal ions

Denaturing agents include: Transition metal ions such as Pb2+, Hg2+, and Cd2+ form water-insoluble salts with –SH groups; Hg2+ for example forms –S–Hg–S–.

Alcohols

Denaturing agents include: 70% ethanol penetrates bacteria and kills them by coagulating their proteins. It is used to sterilize skin before injections.