1. Amino Acids Proteins, and Enzymes
Types of Proteins
Amino Acids
The Peptide Bond

2. Types of Proteinsوظائف البروتينات
Type Examples
Structural tendons, cartilage, hair, nails
Contractile muscles
Transport hemoglobin
Storage milk
Hormonal insulin, growth hormone
Enzyme catalyzes reactions in cells
Protection immune response

3. Amino Acids Building blocks of proteinsوحدات بناء البروتين
Carboxylic acid groupتحوي على
Amino group
Side group R gives unique characteristics
R side chain I
H2H—C —COOH H

4. Description – general properties
Amino acids are derivatives of carboxylic acids formed by substitution of -hydrogen for amino functional group.

6. Structure
a-carbon

7. Amino Acids Building Blocks of Proteins

8. Amino Acids
Amino acids are the structural building blocks (monomers) of proteins.وحدات أولية من الأحماض الامينية لبناء البروتينات
There are twenty different kinds of amino acids used in proteins.عشرين حامض اميني في بناء البروتينات
Proteins are referred to as heteropolymers due the variety of amino acids involved in their structure. البروتينات بوليمر متعدد يحتوي على أحماض امينية مختلفة التركيب

9. BASICS
Lets start with the basics. All amino acids have a common structural unit that is built around the alpha carbon (click 1). Lets call this the “core” structure. The figure shows the core with one of the bonds on the -carbon unassigned. A group in this location is represented by the letter R (click 1).
COOH C
+H3N  H R R
R groups are the only variable groups in the structure. Consider R the only unknown and focus on this group to learn the structures. Hence, Rule (1) is amino acids are composed of a core group and an R group. Rule (2) is the R group gives an amino acid its structural identity and, later as we will see, its unique biochemical properties.

10. Examples of Amino AcidsH I
H2N—C —COOH
H glycine
CH3
H alanine

11. Amino Acids (cont’d.)
The repeating sequence of atoms along a proteins is referred to as the polypeptide backbone. Attached to this repetitive chain are the different amino acid side chains (R-groups) which are not involved in the peptide bond but which give each amino acid its unique property.

12. insulin chemical structure

13. Amino Acids (cont’d.)
Amino acids, like carbohydrates, show isomerism. Proteins are only made up of amino acids which are L-isomers.
D-isomer
L-isomer

14. AA are optically active molecules and asymmetry of their mirror images is not superimposable (except in the case of glycine where the R-group is hydrogen)
according new UIPAC nomenclature L- D- forms were replaced for (S)- and (R)- system

16. Types of Amino Acids Nonpolar R = H, CH3, alkyl groups, aromatic O
Polar ll
R = –CH2OH, –CH2SH, –CH2C–NH2,
(polar groups with –O-, -SH, -N-)
Polar/Acidic
R = –CH2COOH, or -COOH
Polar/ Basic
R = –CH2CH2NH2

17. Properties of Amino Acids
High melting points, over 200C
More soluble in water than in ether.
Larger dipole moments than simple acids or simple amines.
Less acidic than most carboxylic acids, less basic than most amines.
pKa = 10
pKb = 12
=>
Chapter 24

18. Complete Proteins Provide all the essential amino acids.
Examples: those in meat, fish, milk, eggs.
Plant proteins are generally incomplete.
Vegetarians should eat many different kinds of plants, or supplement diet with milk or eggs مصادر البروتينات الغذائية =>
Chapter 24

20. 20 Common Amino Acids
You should know names, structures, pKa values, 3-letter and 1-letter codes
Non-polar amino acids
Polar, uncharged amino acids
Acidic amino acids
Basic amino acids

21. Amino Acids (cont’d.)
Amino acids are grouped according to whether their side chains are:-
acidic
basic
uncharged polar
non polar

22. Acidic Amino Acids Aspartic Acid asp D Acidic Polar Aspartic Acid asp
                                   
Acidic
Polar 
Aspartic Acid asp
  Acidic
Polar 
Glutamic Acid glu Acidic
Polar
Acidic Amino Acids

23. Lysine lys 
Basic
Polar
 Arginine arg
  Basic
Polar
Basic Amino Acids

24. Neutral Polar Amino Acids
Glutamine gln Neutral
Polar
Tyrosine  tyr   Neutral
Polar
Neutral Polar Amino Acids

25. Non Polar Amino Acids Isoleucine ile Neutral Non-polar Methionine met

26. Amino Acids (cont’d.)
The type of side chain is very important as it affects the solubility of the amino acid.
Hydrophobic features include long non-polar (uncharged) chains or complex aromatic rings.
Hydrophilic features include additional carboxyl groups or amino groups not involved in peptide bonding which are ionised in solution.

27. Essential Amino Acids 10 amino acids not synthesized by the body
arg, his, ile, leu, lys, met, phe, thr, trp, val
Must obtain from the diet
All in diary products
1 or more missing in grains
and vegetables

28. Essential Amino Acids Arginine (Arg) Threonine (Thr) Lysine (Lys)
Valine (Val)
Phenylalanine (Phe)
Tryptophan (Trp)
Methionine (Met)
Histidine (His)
Leucine (Leu)
Isoleucine (Ile) =>
Chapter 24

29. Amino Acids (cont’d.)
At neutral pH’s amino acids exist in an ionised form and have both acidic and basic properties. This is because the carboxylic group donates hydrogen ions to the solution (acidic) whereas the amino group (NH2) attracts hydrogen ions from the solution.

30. Zwitterion Amino acid exists as a dipolar ion.
-COOH loses H+, -NH2 gains H+.
Actual structure depends on pH =>
Chapter 24

31. Amino Acids as Acids and Bases
Ionization of the –NH2 and the –COOH group
Zwitterion has both a + and – charge
Zwitterion is neutral overall +
NH2–CH2–COOH H3N–CH2–COO–
glycine Zwitterion of glycine

32. Isoelectric Point
pH at which amino acids exist as the zwitterion (neutral).
Depends on structure of the side chain.
Acidic amino acids, isoelectric pH ~3.
Basic amino acids, isoelectric pH ~9.
Neutral amino acids, isoelectric pH is slightly acidic, =>
Chapter 24

33. pH and ionization H+ OH– + + Positive ion zwitterion Negative ion
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–
Positive ion zwitterion Negative ion
Low pH neutral pH High pH

34. Zwitterionic structure is neutral and its value of pH is called isoelectric point.

35. Structure and pH
=>
Chapter 24

36. Structure of Peptide The peptide bond is an amide bond.
Amides are very stable and neutral.
=>
Chapter 24

37. Peptide Bond Formation
The amino group of one molecule condenses with the acid group of another.
Polypeptides usually have molecular weight less than 5000.
Protein molecular weight ,000, =>
Chapter 24

38. Learning Check AA1 A. NH2–CH2–COOH (Glycine) CH3 | CH–OH
Identify each as (1) polar or (2) nonpolar
A. NH2–CH2–COOH (Glycine)
CH3 |
CH–OH
B. NH2–CH–COOH (Serine)

39. Solution AA1 A.(2) NH2–CH2–COOH (Glycine) CH3 | CH–OH
Identify each as (1) polar or (2) nonpolar
A.(2) NH2–CH2–COOH (Glycine)
CH3 |
CH–OH
B. (1) NH2–CH–COOH (Serine)

40. Amino Acids (cont’d.)
Amino acids link together by covalent peptide bonds. This involves a condensation /dehydration reaction. These bonds are very strong. When this takes place the charged amino and carboxylic groups disappear.

41. Learning Check AA2 CH3 CH3 + H3N–CH–COOH H2N–CH2–COO– (1) (2)
(1) (2)
Select from the above structures
A. Alanine in base.
B. Alanine in acid.

42. Solution AA2 CH3 CH3 + H3N–CH–COOH H2N–CH2–COO– (1) (2)
(1) (2)
Select from the above structures
(2) Alanine in base.
(1) Alanine in acid.

43. The Peptide Bond
Amide bond formed by the –COOH of an amino acid and the –NH2 of the next amino acid
O CH3
| | |
NH3–CH2–COH H3N–CH–COO–
O CH3
| | |
NH3–CH2–C – N–CH–COO–
| peptide bond H

45. Peptides Amino acids linked by amide (peptide) bonds
Gly Lys Phe Arg Ser
H2N COOH
end Peptide bonds end
Glycyllysylphenylalanylarginylserine

46. Primary Structure of Proteins
The particular sequence of amino acids that is the backbone of a peptide chain or protein
Ala-Leu-Cys-Met

47. Learning Check AA3
What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

48. Solution AA3
Tripeptides possible from one each of leucine, glycine, and alanine
Leu-Gly-Ala
Leu-Ala-Gly
Ala-Leu-Gly
Ala-Gly-Leu
Gly-Ala-Leu
Gly-Leu-Ala

49. Learning Check AA4
Write the three-letter abbreviations for the following tetrapeptide:

50. Solution AA4
Ala-Leu-Cys-Met

51. Hydrolysis of a Dipeptide

52. Learning Check P4
What are the products of the complete hydrolysis of Ala-Ser-Val?

53. Solution P4 The products of the complete hydrolysis of Ala-Ser-Val are
alanine
serine
valine

54. Test Your Knowledge. Click to see the answer.
Q: What amino acid has the shortest carbon chain in its R group?
A: Glycine. It has no carbon in its R group.
Q: What structural feature is common to alanine, serine and cysteine?
A: All three have a single carbon in their R groups.
Q: Which amino acid has the longest straight chain of carbons in its R group?
A: Lysine. It has 4. Leucine and isoleucine have 4 but their chains are branched
Q: What R group structural feature is common to phenylalanine, tyrosine, tryptophan, and histidine?
A: All four have rings that are attached to the core via a –CH2 group
Q: What structural feature is common to isoleucine and threonine
A: Both have an asymmetric carbon in their R group

55. Peptide Bond Formation
The amino group of one molecule condenses with the acid group of another.
Polypeptides usually have molecular weight less than 5000.
Protein molecular weight ,000, =>
Chapter 24

56. الأحماض للامينية المتحدة معا العدد تسعة تذكر في لتسمية عدد الأحماض الامينية المتحدة من العدد عشرة إلى العدد تسعة وتسعين تسمى بولي ببتايد إما إذا عدد الأحماض المتحدة من مائة وأكثر تسمى بروتين

57. Classification of Proteins
Simple: hydrolyze to amino acids only.
Conjugated: bonded to a nonprotein group, such as sugar, nucleic acid, or lipid.
Fibrous: long, stringy filaments, insoluble in water, function as structure.
Globular: folded into spherical shape, function as enzymes, hormones, or transport proteins =>
Chapter 24

58. Levels of Protein Structure
Primary: the sequence of the amino acids in the chain and the disulfide links.
Secondary: structure formed by hydrogen bonding. Examples are -helix and pleated sheet.
Tertiary: complete 3-D conformation.
Quaternary: association of two or more peptide chains to form protein =>
Chapter 24

59. Alpha Helix
Each carbonyl oxygen can hydrogen bond with an N-H hydrogen on the next turn of the coil.
=>
Chapter 24

60. Pleated Sheet Each carbonyl oxygen hydrogen
bonds with an N-H hydrogen on an
adjacent peptide chain.
=>
Chapter 24

61. Summary of Structure
=>
Chapter 24

62. Denaturation
Disruption of the normal structure of a protein, such that it loses biological activity.
Usually caused by heat or changes in pH.
Usually irreversible. A cooked egg cannot be “uncooked.” =>
Chapter 24