1. Chapter 19, Unnumbered Figure 1, Page 701

2. Amino acids
Contain a carboxylic acid group and an amino group on the alpha () carbon.
Each contain a different side group (R).
The nonionized form shows no charges.
In aqueous neutral solution they exist as the zwitterion.
In the solid state AAs exist exclusively as zwitterions.
Are chiral except for glycine (R=H).
Fischer projections show that they posses stereoisomerism. Specifically that they can exist as enantiomers.
With very rare exceptions, only the L-∝-amino acids exist in plants and animals.
It is not necessary to specify the L-configuration since D-amino acids are rarely found (usually antibiotics and microbial structures)
Figure UN
Title:
General Structure of an α-Amino Acid
Caption: .

3. Hydrophilic = tending to dissolve in water Hydrophobic = “ not to “
More than 20 AAs are found in different organisms but only what Francis Crick has called the “magic 20” are used for protein synthesis.
IUPAC names are rarely used
common names
2-aminoacetic acid
glycine
2-aminopropanoic acid
alanine
2-amino-3-methylbutanoic acid
valine
Two types of abbreviations:
Three-letter codes (older) and one-letter abbreviations (newer) are commonly used in peptides and proteins.
Chapter 19, Table 19.2
Hydrophilic = tending to dissolve in water
Hydrophobic = “ not to “
When negatively physiological pH:
Aspartate & glutamate
Can exist as amides

4. (-) Less acidic In solution, the zwitterion can change based on pH.
The pH at which the zwitterion exists is called the isoelectric point, pI.
In solution, depending on the pH, there is an equilibrium between 3 species: zwitterion, cation, and anion. 14 13 12 11 10 9 8 7 6 5 4 3 2 1
H2N–CH2–COO-
negative ion = carboxylate ion form
(at high pH)
pH > pI
(-) Less acidic
OH−
Chapter 19, Unnumbered Figure 3, Page 676 O ║
H3N+—CH2—C—O–
Zwitterion of glycine
H3N+–CH2–COO-
zwitterion
(at pI) H+
(+) more acidic
H3N+–CH2–COOH
positive ion = ammonium ion form
(at low pH)
pH < pI

5. Example What form of glutamic acid would you expect to predominate in:
(a) strongly acidic solution?
(b) strongly basic solution?
(c) at its isoelectric point (pI 3.2)?

6. Separation of Amino Acids
Electrophoresis
In electrophoresis, an electric current is used to separate a mixture of amino acids.
The positively charged amino acids move toward the negative electrode.
The negatively charged amino acids move toward the positive electrode.
An amino acid at its pI does not migrate.
The amino acids are identified as separate bands on the filter paper or thin layer plate.
Paper chromatography
A mixture of amino acids can also be separated on the basis of polarity.

7. Essential Amino Acids
Adequate amounts of 11 of the 20 can be synthesized (by adults) from carbohydrates and lipids in the body if a source of nitrogen is also available.
Because the human body is incapable of producing or producing enough of 9 of 20, these are called Essential Amino Acids
Essential amino acids
Are in meat and diary products.
Are missing (one or more) in grains and vegetables.
Certain traditional dishes, such as Mexican corn and beans, Japanese soybeans and rice, and Cajun red beans and rice, contain one ingredient which compensates for the lack of essential amino acids in the other in order to fulfill the needs of a complete protein.

8. Proteins are polymers of amino acids. Up to 50.  peptide 50-100
Proteins are polymers of amino acids. Up to 50  peptide  polypeptide > 100  protein Proteins are the workhorse molecules in living organisms and are involved in virtually all facets of cell structure and function.
Figure 19-T01
Title:
Classification of Some Proteins and Their Functions
Caption:
Insulin = 51 AAs = hormone
Sucrase = 1827 AAs = enzyme

9. Linked by a peptide bond
The peptide bond is an amide bond whose origin is from amino acids.
Forms between the carboxyl group of one amino acid and the amino group of another amino acid.
Di = 2 AAs
Linked by a peptide bond
Figure UN
Title:
Formation of Peptides
Caption:
A chain of five amino acids is a pentapeptide, and longer chains of amino acids form polypeptides. We can write the amidation reaction for the zwitterion forms of two amino acids as follows.
Tri = 3 AAs
Linked by a peptide bond

10. A polypeptide chain starts with N and ends with C.
starting with the N-terminal amino acid add -yl ending to every AA in the chain
Until you get to the last one, at the C-terminal, and provide its full name.
Because amino acids have two functional groups, amide bond formation with a mixture of two amino acids affords four products:
Figure UN
Title:
Alanylglycylserine
Caption:
In the name of a peptide, each amino acid beginning from the N terminal end has the ine (or ic acid) replaced by yl. The last amino acid at the C terminal end of the peptide has its full name. For example, a tripeptide consisting of alanine, glycine, and serine is named as alanylglycylserine. For convenience, the order of amino acids in the peptide is often written as the sequence of three-letter abbreviations.

11. The primary structure of a protein is
The particular sequence of amino acids.
The backbone of a peptide chain or protein.
Insulin was the first protein to have its primary structure determined (sequencing)
Has a primary structure of two polypeptide chains linked by disulfide bonds.
Has chain A with 21 amino acids and chain B with 30 amino acids.
Insulin, the hormone that regulates blood-glucose levels.
The British biochemist Frederick Sanger determined the primary structure of the protein hormone insulin in 1953 after 8 years of work.
Awarded the Noble Prize in chemistry in 1958 for this work.
Awarded a second Noble Prize in chemistry in 1980 for his work on sequencing of units in nucleic acids.

12. Pituitary gland secretions include:
The nonapeptides oxytocin and vasopressin
Have similar primary structures.
Differ only in the amino acids at positions 3 and 8.
Oxytocin and vasopressin are peptide hormones. Both are produced by the pituitary gland.
Pituitary gland secretions include:
growth hormone (which stimulates cellular activity in bone, cartilage, and other structural tissue)
thyroid stimulating hormone (which causes the thyroid to release metabolism-regulating hormones)
antidiuretic hormone (which causes the kidney to excrete less water in the urine)
prolactin (which stimulates milk production and breast development in females)
The pituitary gland is influenced both neurally and hormonally by the hypothalamus.
Figure UN
Title:
Oxytocin and Vasopressin
Caption:
Polypeptides in the Body

13. Two Types of β-Pleated Sheets
Secondary Structure – indicate the three-dimensional spatial arrangements of the polypeptide chains.
β-pleated Sheet
Consists of polypeptide chains arranged side by side.
Has hydrogen bonds between chains.
Has R groups above and below the sheet.
Is typical of fibrous proteins such as silk.
Two Types of β-Pleated Sheets

14. A ribbon model of a protein
Random coil or loop
Chapter 19, Unnumbered Figure 4, Page 690

15. The tertiary structure of a protein
Is defined by the primary structure
Gives a specific three dimensional shape to the polypeptide chain.
Involves interactions and cross links between different parts of the peptide chain.
Tertiary structures are stabilized by:
Hydrophobic and hydrophilic interactions.
Salt bridges.
Hydrogen bonds.
Disulfide bonds.

16. The quaternary structure
Is the combination of two or more tertiary units.
Is stabilized by the same interactions found in tertiary structures.
Of hemoglobin consists of two alpha chains and two beta chains. Alpha has 141 AA residues, beta has 146 AA residues.
The heme group in each subunit picks up oxygen for transport in the blood to the tissues.
Hb also plays an important role in removing CO2
Adult hemoglobin HbA

17. Summary of Protein Structures

18. Fibrous protein - peptide chains are arranged in long strands or sheets. Such proteins have long rodlike structures that can intertwine with one another and form strong fibers.
They are generally water-insoluble, usually used to construct connective tissues, tendons, bone matrix and muscle fiber.
On the basis of structural features, proteins are classified into two major types:
Globular protein – Soluble polypeptide chains folded into spherical shapes. Generally involved in cell function: synthesis, transport and metabolism.
Carry out synthesis, transport, and metabolism in the cells.
May serve as enzymes, hormones, or antibodies.
Such as myoglobin store and transport oxygen in muscle.

19. Fibrous protein 3 basic types Keratins Elastins Collagens
They form the hard but non-mineral structures in reptiles, birds, amphibians and mammals.
fibers are strong, provide a structural role in nature.
 They are the main constituent of structures that grow from the skin:
hair & fingernails
feathers, horns, claws, hooves
alpha keratins -in the hair (including wool), horns, nails, claws and hooves of mammals contain large amounts of 𝛼−helix structures.
beta keratins -in the scales and claws of reptiles, their shells (chelonians, such as tortoise, turtle, terrapin), and in the feathers, beaks, and claws of birds contain large amounts of 𝛽-pleated sheet structures.
Fibrous protein
3 basic types
Elastins
 fibers are elastic, provide flexibility to structures.
 skin, blood vessels, lungs, intestines, tendons,& ligaments
Collagens
 main structural protein in the body, provide rigidity of connective tissue in skin, tendons, bones, cartilage and ligaments.

20. Protein hydrolysis
Splits the peptide bonds to give smaller peptides and amino acids.
In the lab, the hydrolysis of a peptide requires acid or base, water and heat.
In the body, enzymes catalyze the hydrolysis of proteins.
Occurs in the digestion of proteins.
Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues.
Protein denaturation
involves the disruption of bonds in the secondary, tertiary and quaternary protein structures.