The document covers the importance, characteristics, and functions of amino acids and proteins, highlighting their roles as building blocks for proteins and their involvement in various biological processes. It discusses the structural levels of proteins, including primary, secondary, and tertiary structures, and details the classification of amino acids including essential and non-essential types. Furthermore, it mentions the history of amino acids, their classification based on charge and polarity, and the presence of uncommon amino acids with specialized functions.

1. EVELYN HONE COLLEGE OF APPLIED SCIENCE AND
TECHNOLOGY
SCHOOL OF HEALTH SCIENCES
DEPARTMENT OF BIOMEDICAL SCIENCES
METABOLIC BIOCHEMISTRY
Dr. G.H Msoni

2. OBJECTIVES
• By the end of the topic, students must;
• Define amino acids
• Know the various classes of amino acids
• Know the function of amino acids
• Know the uncommon amino acids
• Define proteins
• Know the function of proteins
• Know the levels of protein structure

3. AMINO ACIDS:
CHARACTERISTICS & FUNCTIONS
3

4. OUTLINE
• Importance of Amino Acids
• History of Amino Acids
• Zwitterion
• Chirality
• General properties conferred by side chain
• Groupings of amino acids
• Uncommon amino acids
• Essential and Non-essential amino acids
4

5. 5
BIOMEDICAL IMPORTANCE OF AMINO ACIDS
 units or building blocks for polypeptide chains of proteins.
 Amino acids and their derivatives participate in cellular
functions such as nerve transmission and biosynthesis of
porphyrins, purines, pyrimidines and urea.
 Short polymers of amino acids called peptides perform
prominent roles in the neuroendocrine system as hormones,
hormone-releasing factors, neuro-modulators, or neuro-
transmitters.

6.  In nature there are over 300 naturally occuring amino acids
 Only 20 of these occur in proteins(std amino acids)
 Some proteins contain amino acid derivatives that are
generated after incorporation of the amino acid into the protein
molecule
 Several free L-α-amino acids fulfill important roles in metabolic
processes. Examples include:
-ornithine, citrulline, & argininosuccinate that
participate in urea synthesis;
-tyrosine in formation of thyroid hormones;
- glutamate in neurotransmitter biosynthesis.
6

7.  Nineteen of these are α-amino acids with a primary amino
group (–NH3+) and a carboxylic acid (carboxyl; –COOH)
group attached to a central carbon atom.
 This is called the α-carbon atom (C) because it is adjacent to
the carboxyl group. Also attached to the C atom is a hydrogen
atom and a variable side-chain or ‘R’ group.
EXCEPTION to this general structure is proline, which has a
secondary amino group hence is an α-imino acid.
7

8. HISTORY
• The first to be discovered was asparagine, in 1806. The last of
the 20 to be found, threonine, was not identified until1938.
• All the amino acids have trivial or common names, in some
cases derived from the source from which they were first
isolated.
• Asparagine was first found in Asparagus spp,
• Glutamate in wheat gluten;
• Tyrosine was first isolated from cheese (its name is derived
from the Greek tyros, “cheese”);
• Glycine (Greek glykos, “sweet”) was so named because of its
sweet taste.
• The names of the amino acids are often abbreviated, either to
three letters or to a single letter.
8

9. 9
Amino acids may have positive, negative or zero
charge (Zwitterions).
An α- amino acid consists of - an amino group
- a carboxyl group
- a hydrogen atom
- a distinctive R group
(side chain)
All bonded to an α-
carbon. This carbon
atom is called α- carbon
because its adjacent to
the carboxyl (acidic)
group
NH2
C
H CO OH
N H3
C
H CO O
R R
–
Dipolar ion (Zwitterion)
form of an amino acid
Un-ionized form of an
amino acid
**Amino acids in solution at physiologic pH (pH 7.4) are predominantly
dipolar where the amino group is protonated (–NH3
+
) and the carboxyl group is
dissociated (–COO-
)**
**Biological pH is 7.00**.
+

10. • All of the amino acids, except for glycine, have four different
groups arranged tetrahedrally around the central C atom.
• This is known as an asymmetric center or chiral center and
has the property of chirality.
• Because of the tetrahedral arrangement of the bonding
orbitals around the α-carbon atom, the four different groups
can occupy two unique spatial arrangements-hence two
possible stereoisomers.
• Since they are non-superimposable mirror images of each
other, the two forms represent a class of stereoisomers called
enantiomers
10

11. • The standard 20 amino acids differ only in the structure of the
side-chain or amino acids ‘R’ group.
• Are subdivided into smaller groupings on the basis of
similarities in the properties of their side-chains.
• They display different physiochemical properties
• Some are acidic; others are basic.
• Some have small side-chains, others large, bulky side-chains.
Some have aromatic side-chains, others are polar.
• Some confer conformational inflexibility.
• Others can participate either in hydrogen or covalent bonding.
• **Some are chemically reactive.** 11

12. • The charged functional groups confers property of solubility
in—polar solvents such as water and ethanol and insolubility in
nonpolar solvents such as benzene, hexane, or ether.
• High amount of energy required to disrupt the ionic forces
that stabilize the crystal lattice account for the high melting
points of amino acids (> 200 °C).
• Amino acids do not absorb visible light and thus are
colourless. However, tyrosine, phenylalanine, and especially
tryptophan absorb high-wavelength (250–290nm) ultraviolet
light.
• Tryptophan therefore makes the major contribution to the ability
of most proteins to absorb light in the region of 280 nm.
12

13. 13
H CH
NH
COO
3
+
–
Aliphatic side chains
C H
NH
COO
CH 3
3
+
–
CH
NH
COO
H
C
CH3
CH3 +
3
–
CH
NH
COO
CH2
C H
CH3
CH3
3
+
–
C H
NH
COO
CH
CH2
CH3
CH3 +
3
–
Glycine
Alanine
Valine
Leucine
Isoleucine
Chemically unreactive and
have hydrophobic side
chain-have aversion to
water and like to cluster.
Occur primarily in the
interior of cytosolic
proteins.
Smallest & simplest structured amino
acid owing to H-atom-does not exist
exhibit chirality. Often occurs where
peptides bend sharply.

14. 14
Amino acids containing hydroxyl (OH) side chains
CO O
H
C
NH
CH2
OH
–
3
+
Serine
C H CO O
NH
H
C
OH
CH3
+
3
3
–
–
Threonine
Side chains containing sulfur atoms
CH CO O
NH
CH2
H
3
+
S
C H CO O
N H
CH2
CH2
CH3
S
+
–
Methionine
Cysteine
Contains a sulfhydryl group (-SH). ?
Hydrophobic. -SH is highly reactive capable
of reacting with another cysteine to form a
disulfide bond. The primary thio (–SH)
group is a nucleophiles and can function
during enzymatic catalysis
Contains a sulfur atom in a thioester
linkage (-S-CH3). Is Hydrophobic
Hydroxylated. More hydrophilic and reactive
than alanine.The primary alcohol group is a
nucleophile that can function during
enzymatic catalysis
Hydroxylated. More hydrophilic and
reactive than valine
**The –OH groups of these amino acids can participate in enzyme regulation**

15. 15
Side chains containing acidic groups on their amides
CO O
H
C
NH
CH2
C
O
O
CO O
H
C
NH
CH2
CO O
H
C
NH
CH2
CO O
H
C
NH
CH2
C
O
NH2
CH2
C
O
O
CH2
C
O
NH2
3
3
–
–
–
–
+
+
+
+
3
3
–
–
Aspartic acid
Asparagine
Glutamic acid
Glutamine
Uncharged derivatives of glutamate and aspartate are glutamine and
asparagine respectively, which contain a terminal amide group in place of a
carboxylate
Side chain nearly always negatively
charged at physiological pH.
Side chain nearly always negatively
charged at physiological pH.
• Are therefore polar and de-
protonated amino acids.
• The charged R groups
stabilize specific protein
conformation via ionic
interactions, or salt bonds

16. 16
Side chains containing basic groups
CH CO O
CH 2
CH2
CH2
N
C NH2
NH2
N H
CH CO O
CH2
CH2
CH2
NH
CH CO O
CH2
N H
CH2
NH
N
N
H
H
+
–
3
+
–
3
+
–
3
Arginine
Lysine
Histidine
Equally polar and hydrophilic
but may be positively charged
at neutral pH depending on
conditions. Plays an important
role in enzymatic catalysis
functioning as either a base or
an acid catalyst at pH 7.0
3
+
+
Very polar side chains
which render them highly
hydrophilic. Are positively
charged at neutral pH.
The charged R groups stabilize specific protein conformation
via ionic interactions, or salt bonds

17. 17
Side chains containing aromatic rings
H CO O
CH2
NH
O
H H CO O
NH
CH2
CH2 H CO O
NH
N
H
C
C
C
Phenylalanine
Tyrosine
Tryptophan
Imino acid
CO O
N
H
–
3
+
–
3
+
–
2
+
–
3
Proline +
Phenyl ring attached to a
methylene group. Hydrophobic
Contains a -OH group which
makes it less hydrophobic than
Phe (F). OH is also reactive,
paticipates in enzyme regulation.
Indole ring joined to a
methylene group.
Hydrophobic
Has an aliphatic side chain bonded to both the
nitrogen and α carbon atoms. It is hydrophobic
but, with its aliphatic side-chain bonded back on to
the amino group, it is conformationally rigid. Often
found on bends of folded proteins.
Occur primarily in the interior of cytosolic proteins The aromatic rings contain
delocalised electron clouds which enable them to interact other systems and
transfer electrons. They absorb high-wavelength (250– 290 nm) ultraviolet light.

18. 18
Non polar amino acids Polar amino acids
Alanine,Ala,A Arginine,Arg,R
Isoleucine,Ile,I Asparagine,Asn,N
Leucine,Leu,L Aspartic acid,Asp,D
Methionine,Met,M Cysteine,Cys,C
Phenylalanine,Phe,F Glutamic acid,Glu,E
Proline,Pro,P Glutamine,Gln,Q
Tryptophan,Trp,W Glycine,Gly,G
Valine,Val,V Histidine,His,H
Lysine,Lys,K
Serine,Ser,S
Threonine,Thr,T
Tyrosine,Tyr,Y
Please note the three letter and one letter abbreviation for
each 19 amino acids and 1 imino acid.

19.  Humans can synthesize 12 of the 20 common amino acids from
the amphibolic intermediates of glycolysis and the citric acid cycle
- 9 from amphibolic intermediates
- 3 (cysteine, tyrosine and hydroxylysine) from
nutritionally essential amino acids
Essential amino acids must be supplied in the diet
Essential Non-essential
Arginine* Alanine
Histidine Asparagine
Isoleucine Aspartate
Leucine Cysteine*
Lysine Glutamate
Methionine Glutamine*
Phenylalanine Glycine*
Threonine Proline*
Tryptophan Serine
Valine Tyrosine*
19

20. 20
Uncommon Amino Acids Also Have Important Functions
In addition to the 20 common amino acids, proteins may contain
residues created by modification of common residues already
incorporated into a polypeptide:
a)4-hydroxyproline, a derivative of proline, found in plant cell
wall proteins, collagen
b)5-hydroxylysine, derived from lysine-also found in collagen.
c) 6-Nmethyllysine, is a constituent of myosin, a contractile
protein of muscle.
d)carboxyglutamate, found in the blood clotting protein
prothrombin and in certain other proteins that bind calcium ions as
part of their biological function.

21. e)more complex,desmosine, a derivative of four L residues,
which is found in the fibrous protein elastin.
f)Selenocysteine is a special case. This rare amino acid residue
is introduced during protein synthesis rather than created through
a post-synthetic modification. It contains selenium rather than
the sulfur of cysteine. Actually derived from serine. Is a constituent
of just a few known proteins.
g)Some 300 additional amino acids have been found in cells.
They have a variety of functions but are not constituents of
proteins. E.g. Ornithine and citrulline.
21

22. 22
Amino Acids Can Act as Acids and Bases
When an amino acid is dissolved in water, it exists in solution as the
dipolar ion, or zwitterion (German for “hybrid ion)
A zwitterion can act as either an acid (proton donor):
OR

23. a base (proton acceptor):
23

24. ANY
QUESTIONS ???????
???????????????????
24

25. TRANSAMINATION AND DEAMINATION

26. 26
Proteins-
Characteristics & Functions

27. 27
Biological Functions
1. Enzyme catalysts
Nearly all chemical reactions in biological systems are
catalyzed by enzymes-nearly all known enzymes are
proteins
2. Transport and storage
Many small molecules and ions are transported by specific proteins
eg Haemoglobin transports oxygen
Iron is stored in the liver as ferritin
Lipoproteins transports fats, steroids, phosholipids
3. Coordinated motion
Muscle contraction is accomplished by sliding motion of two kinds
of protein filaments-actin & myosin

28. 28
Biological Functions Cont…….
4. Mechanical/Structural support
Tensile strength of the skin and bone-due to the presence of
collagen
5. Immune/Defence Proteins
Antibodies/immunoglobulins
6. Generation and transmission of nerve impulses
Receptor proteins play a role in transmission of impulses
7. Control of growth and differentiation
-Growth factor proteins play a role in growth and differentiation
-Hormones coordinate activities of different cells in multicellular
organisms

29. Amino acids sequence determines:
– how a protein folds up into its unique three-dimensional
structure
– and this in turn determines the function of the protein
– cellular location – certain sequences serve as signals that
target proteins for export or tissue distribution
29

30. Levels of Protein Structure
Primary Structure
• Is a linear sequence of amino acids linked together by peptide bonds
or amide bonds-between the α -amino group of one amino acid and
the α-carboxyl group of another.
30
+H3N-serine–leucine–phenylalanine-COO- OR Ser-Leu-Phe
OR S-L-F
Convention has it that peptide chains are written down with the
free α-amino group on the left, the free α-carboxyl group on the
right and a hyphen (-) between the amino acids to indicate the
peptide bonds.

31. -2 amino acids joined by a peptide bond to form a dipeptide
-3 amino acids joined by 2 peptide bond to form a tripeptide
-Upto 25 amino acids -form a oligopeptide
-Peptides with more than 25 amino acid RESIDUES are termed
polypeptides
****If MW is more than 10,000, polypeptides may be referred to as
proteins**** 31

32. Some naturally occurring peptides have biologically important effects
(a)Oxytocin (9 residues)–stimulates uterine contractions
(b)Bradykinin (9 residues)–inhibits inflammation in tissues
(c)Thyrotropin- releasing factor
(d)Mushroom toxin amanitin is also a small peptide, as are some
antibiotics.
Slightly larger peptides include:
(e)Insulin with two polypeptide chains (30 and 21 residues) held
together by disulfide bonds
(f)Glucagon (29 residues) – counters the effects of insulin
32

33. Protein Secondary structure
• Secondary structure in a protein refers to the regular folding of
regions of the polypeptide chain giving rise to recurring structural
patterns. 2° may exhibit few irregularities (e.g. random coils)
Types of 2° Structures
i)α-Helix,
ii)β-Pleated Sheets
iii)Random coils (irregular)
33

34. The α-Helix
34
Is a common protein
secondary structure
The polypeptide is
tightly wound around
an imaginary axis
drawn longitudinally
through the middle of
the helix, and the R
groups of the amino
acids protrude
outward from the
helical backbone

35. • Certain amino acids are more often found in α -helices than others.
• Pro is rarely found in α-helical regions as it cannot form the correct
pattern of hydrogen bonds due to the lack of a hydrogen atom on its
nitrogen atom.
• For this reason, Pro is often found at the end of an α-helix, where it
alters the direction of the polypeptide chain and terminates the helix.
• Different proteins have a different amount of the polypeptide chain
folded up into α-helices. For example, the single polypeptide chain of
myoglobin has eight α-helices.
35

36. 36
• Are stabilized by hydrogen bonding between β strands
• The hydrogen bonds form between the peptide bonds either in different polypeptide chains or in different
sections of the same polypeptide chain.
• The planarity of the peptide bond forces the polypeptide to be pleated with the side-chains of the amino acids
protruding above and below the sheet.
β- pleated sheets

37. 37
.
• The pleated sheet is extended into a zigzag (pleated) formation rather the being tightly coiled
as in the α- helix
• Adjacent polypeptide chains in β-pleated sheets can be either parallel or antiparallel
depending on whether they run in the same direction or in opposite directions, respectively.
• Role of β-pleated sheets is to provide strength and rigidity in many structural proteins, such
as silk fibroin, which consists almost entirely of stacks of antiparallel β-pleated sheets.

38. 38

39. 39

40. 40
β- turns
• In globular proteins, which have a compact structure, nearly one
third of the amino acid residues are in turns or loops where the
polypeptide chain reverses direction making a hairpin or –turn.
- These are the connecting elements that link successive runs of α and
β conformations
In these β-turns, the carbonyl oxygen of one amino acid is
hydrogen bonded to the hydrogen on the amino group of the
fourth amino acid

41. 41
β- turns cont…..
• These turns are often found connecting the ends of antiparallel β-
pleated sheets.
• Regions of the polypeptide chain that are not in a regular secondary
structure are hence said to have a coil or loop conformation.
• About half the polypeptide chain of a typical globular protein will be
in such a conformation.

42. 42
α-helix
β sheets
Random coils
Protein structure showing α-helix and β sheet conformations

43. 43
Protein Tertiary Structure
• Refers to the entire three dimensional conformation of a
polypeptide- it comprises of helices, sheets, bends, turns and loops -
assembled to form domains and how these domains relate spatially
to one another.
• The polypeptide chain folds spontaneously so that the majority of its
hydrophobic side-chains are buried in the interior, and the majority
of its polar, charged side-chains are on the surface.

44. 44
Protein Tertiary Structure cont…..
• Once folded, the three-dimensional, biologically active (native)
conformation of the protein is maintained by:
• i)hydrophobic interactions ii)electrostatic forces,
• iii)hydrogen bonding iv)covalent disulfide (if present)
• The electrostatic forces include salt bridges between oppositely
charged groups.
• Multiple weak van der Waals interactions occur between the tightly
packed aliphatic side-chains in the interior of the protein.

45. 45
Protein Quaternary Structure
• Quaternary structure comprises 2 or more polypeptide chains united
by forces other than covalent bonds ( i.e. not peptide or disulfide
bonds)
• The forces that stabilize these aggregates are hydrogen bonds and
electrostatic bonds formed between residues on the surface of the
polypeptide chains
• Such proteins are called oligomers and the individual polypeptides of
which they are composed are protomers
(monomers or subunits)

46. 46
Protein Quaternary Structure
• The most commonly encountered oligomeric proteins contain 2 or 4
protomers and are termed dimers and tetramers respectively
• Homodimers contain two copies of the same polypeptide chain,
while in a heterodimer the polypeptides differ

47. 47
FOUR LEVELS OF PROTEIN STRUCTURE

48. 48
Some Proteins Contain Chemical Groups Other Than Amino Acids
Proteins with amino acid residues & no other chemical constituents-
simple proteins.
Proteins containing permanently associated chemical components
&amino acids-called conjugated proteins.
The non–amino acid part of a conjugated protein is usually called its
prosthetic group.
Conjugated proteins are classified on the basis of the chemical nature
of their prosthetic groups
For example, lipoproteins contain lipids, glycoproteins contain sugar
groups, and metalloproteins contain a specific metal.

49. HOW PROTEIN
STRUCTURE IS RELATED
TO FUNCTION

50. • The three-dimensional conformation of proteins
correspond with the wide diversity of function.
Typical examples are:
enzymes
collagen
haemoglobin and myoglobin

51. HAVE YOU MET THE SET
OBJECTIVES ??????????????
?????????????
51