1. Principle of Biochemistry
2-Amino Acids and Proteins
Course code: HFB324
Credit hours: 3 hours
Dr. Siham Gritly
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2. Terms should be learned
• Protein; molecule consisting of one or more
polypeptide chains
• amino acid; an amino group and a carboxylic acid
group attached to an ―alpha‖ carbon (α-C); a
hydrogen and a small organic group (e.g., —H, —
CH3, —CH2OH), called an R-group, are also attached
to the α-C
• Amphoteric; organic substance that acts as both an
acid and a base
• chiral compound; molecule that cannot be
superimposed on its mirror image
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3. • Enantiomers; two organic compounds that are
are mirror images; these compounds contain
one or more chiral carbons
• L-amino acid; stereoisomeric form of amino
acids found in proteins
• N-terminus; (of a protein) the free amino end
• peptide bond; linkage between the amino
group of one amino acid and the carboxyl
group of another amino acid
• peptide or polypeptide; a polymer chain of
three or more amino acids
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4. • R-group; (of an amino acid) one of twenty (or
more) different organic groups bonded to the
alpha carbon
• Stereoisomers; molecules with the same
chemical formulae; they differ only in the way the
different attached groups are oriented in space
• Zwitterions; ion with a positive and a negative
charge
• Chirality describes the ability of a molecule to
rotate the plane of polarized light either to the
right (dextrorotatory) or to the left (levorotatory
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5. Composition and nature of proteins;
• Proteins are complex organic compound found
in animal and plant tissues.
• The protein molecules are nitrogen-containing
amino acids, in addition to
carbon, oxygen, and hydrogen.
• some of which are essential in the sense that
humans cannot make them internally
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6. Protein functions
1-Structural function
• -Structural function
Component of all cell membranes
• Component of cytoplasm "cytoskeleton"
• Component of movement or contractile
structures, such as muscle,
• Component of hair, nails horns, etc. (Keratin
is the main protein of these substances)
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7. Protein functions
2-Metabolic functions
• 1-enzymatic function
• Most specialized proteins with catalytic
activity.
• All chemical reactions of organic biomolecules
in cells are catalyzed by enzymes
• Enzymes mainly consist of proteins.
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8. • 2-hormones (Regulatory Proteins)
• Help regulate cellular or physiological activity.
• The cellular response to many hormonal
signals is often mediated by a class of GTP-
binding proteins called G proteins.
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9. • G proteins are important signal transduction
molecules in cells
• transmitting chemical signals originating from
outside a cell into the inside of the cell.
• G proteins activity is regulated by factors that
control their ability to bind to and hydrolyze
guanosine triphosphate (GTP) to guanosine
diphosphate (GDP).
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10. • 3-Immune function (Defense Proteins)
• Defend organisms against invasion by other
species or protect them
• Immunoglobulin or antibodies, are made by
the lymphocytes of vertebrates and can
recognize & precipitate or neutralize invading
bacteria
• Fibrinogen and thrombin are blood clotting
proteins
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11. • 4-Acid base balance buffering agent
• Buffers ; are compounds that recover or (improve) a
change in pH that occur in response to the addition of
alkali or acid to the solution or; A Buffers are
substances that can bind protons
• Intracellular fluids; protein have the most buffering
effect due to its high concentration in the blood.
• Less concentration of protein such as albumin in blood
causes osmotic pressure in blood plasma decrease and
thus fluid leak out into interstitial spaces causing edema
or swelling
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12. edema or swelling
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13. • Protein molecules possess basic and acidic groups
(Amphoteric molecules )which act as H+
acceptors or donors respectively if H+ is added or
removed.
• A solution with a high hydrogen ion
concentration has a low pH and is therefore more
acidic,
• whereas a solution with a low hydrogen ion
concentration has a high pH and is more alkaline
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14. • Protein buffer: COOH (acid) of amino acid
can lose H+ (COO-)
• NH2 (amine) of amino acid can gain H+
(NH3+) (buffering effect)
Dr. Siham GritlyLysine structure 14

15. • 5-transport
• Bind and carry molecules or ions to organs in
the blood plasma.
• Lipoproteins in blood plasma carries lipids
from the live to other organs
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16. • 6-Energy sources
• any amounts above the needed amino acids for
synthesis of tissues are metabolized and degraded.
• *The amino group of amino acid is converted to
urea in the liver and excreted in urine through
urea cycle.
• *carboxylic group of amino acids are converted
to glucose and enter glycolysis pathway for
energy production.
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17. 7-Nutrient and Storage Proteins
• Seeds of many plants store nutrient proteins
required for the growth of the germinating
seedlings.
• Ovalbumin, the major protein of egg
white, and casein the major protein of milk are
examples of nutrient proteins
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18. Denaturation of proteins
• Denaturation is the breakdown of all covalent
bonds causing change in shape and thus loss of
function.
• Denaturation is due to
• -pH
• -temperature
• -salt concentration
• alcohol
• heavy metals
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19. Protein structure
Each protein has a unique shape or conformation. all proteins
are composed exclusively of subunits of amino acids, which join
together in long chains called polypeptides that fold or coil into
the unique shape of the functional protein
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20. 1-Primary structure of proteins
amino acids sequences
• The primary structure of a protein simply
consists of its linear sequence of amino acids;
for example, "alanine-glycine-tryptophan-
serine-glutamate-asparagine-glycine-lysine-…
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21. 2-Secondary structure
• As peptide bonds are formed, aligning the
amino acids, hydrogen bonds form between
different amino acids in the chain.
• This bonding coils the polypeptide into the
secondary structure of the protein, most
commonly the alpha helix,
• The α-helix coils at every 4th amino acid.
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22. 2-Secondary structure
The α-helix coils of protein
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23. Pleated Protein
the polypeptide have portions that lie parallel to each other (held by hydrogen
bonds) instead of in the alpha helix, in which the amino acids’ hydrogen bonds
form a pleated structure. Fibrous proteins have significant pleated structures
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24. 3-Tertiary Structure of protein
• the side chains (the R groups) of amino acids may fold
independently into a functional unit called the domain.
• Domains are connected by the rest of the polypeptide.
• The folding of a protein into its domains is related to
the hydrophilic or hydrophobic properties of its amino
acids.
• Domain formation is part of the tertiary structure or
proteins. globular shape (globulin)
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25. Tertiary Structure of protein
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26. • 5 kind of bonds stabilize tertiary structure
• 1-van der Waals interaction (between
neighboring atoms) Van der Waals forces
include attractions and repulsions between
atoms, molecules, and surfaces
• 2-H-bonds within the chains or between chains
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27. • 3-hydrophobic interactions (between non
polar)
• 4-ionic interactions (between oppositely
charged groups)
• 5-disulphide linkages, the SH groups of two
neighboring cysteines form –s=s bond known
as disulphide linkage. (covalent bond)
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28. Amino acid Cysteine
disulphide linkages
composed of two cysteines linked by a disulfide bond
Amino acid Cysteine
two cysteines linked by a disulfide bond
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29. 4-Quaternary Protein Structure
the structure formed by several protein molecules (polypeptide
chains), usually called protein subunits
• If two or more polypeptide chains join in
aggregate, they form a quaternary
structure, such as in the protein
molecule, hemoglobin.
• Often quaternary proteins are complexed with
a different molecule, often a mineral.
Hemoglobin contains iron, for example.
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30. 4-Quaternary Protein Structure
Haemoglobin structure
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31. Amino acid
the building block
of proteins
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32. Amino Acid
General structure of amino acid
The carbon atom next to the carboxyl group is called the α
carbon and amino acids with a side-chain bonded to this carbon
are referred to as alpha amino acids. These are the most common
form found in nature.
Lysine structure
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33. Amino acids
• Amino acids contain Carbon,
Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur
• Amino acids have two function groups (both of which are
typically in the ionized form)
• 1- NH2 Amino functional group
• 2-COOH Carboxyl functional group
• Both functional groups attach to a specific carbon, the
alpha α carbon, of the carbon chain. The third bonding site
of the alpha carbon is typically Hydrogen.
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34. • The alpha carbon will have at its fourth
bonding site a side chain, or R group which
gives the amino acid its unique structure and
properties.
• There are 20 + different amino acids in
protein. All have a common structure except
for the R group.
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35. • Some amino acids have R groups that are polar
(hydrophilic), interact with water at physiological pH
(O, N)
• some R groups are nonpolar (and hydrophobic C, H),
• some have acidic side chains pKa < the physiological
pH 7.4. (generally with a negative charge) and some are
basic pKa > the physiological pH 7.4
• pKa acid-ionization constant or acidity constant
• measure of the strength of an acid in solution
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36. • Some with Amino Acids with Aliphatic R-
Groups nonpolar and hydrophobic
(Hydrophobicity increases with increasing
number of C atoms in the hydrocarbon chain)
• Aromatic Amino Acids with benzene ring are
relatively nonpolar. aromatic amino acids
absorb ultraviolet light.
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37. • • Amino acids are joined together by a
dehydration synthesis of amino/carboxyl
groups forming a peptide bond.
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38. α-Amino Acids structure Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC
| info @ themedicalbiochemistrypage.org
pK1 pK R
Amino pK2
Q Acid
Symbol Structure* (COO
H)
(NH2)
Grou
p
Amino Acids with Aliphatic R-Groups
nonpolar and hydrophobic (C )
Glycine Gly – G 2.4 9.8
Alanine Ala – A 2.4 9.9
Valine Val – V 2.2 9.7
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39. α-Amino Acids Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC
| info @ themedicalbiochemistrypage.org
Leucin Leu
2.3 9.7
e –L
Isoleuci Ile –
2.3 9.8
ne I
Non-Aromatic Amino Acids with Hydroxyl R-Groups
Ser –
Serine 2.2 9.2 ≈13
S
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40. α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org
Threonine Thr – T 2.1 9.1 ≈13
Amino Acids with Sulfur-Containing R-Groups
nonpolar and hydrophobic
Cysteine Cys – C 1.9 10.8 8.3
Methionine Met – M 2.1 9.3
Acidic Amino Acids and their Amides
Acidic Amino Acids and their Amides Acidic amino acids are polar and negatively
charged at physiological pH. Both acidic amino acids have a second carboxyl group
hydrophilic
Aspartic Acid Asp – D 2.0 9.9 3.9
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41. α-Amino Acids Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC
| info @ themedicalbiochemistrypage.org
Asparagin
Asn – N 2.1 8.8
e
Glutamic
Glu – E 2.1 9.5 4.1
Acid
Glutamine Gln – Q 2.2 9.1
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42. α-Amino Acids Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC
| info @ themedicalbiochemistrypage.org
Basic amino acids
Arginine Arg – R 1.8 9.0 12.5
Lysine Lys – K 2.2 9.2 10.8
Histidine His – H 1.8 9.2 6.0
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43. α-Amino Acids Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org
Amino Acids with Aromatic Rings
cyclic side groups (benzene ring)
Phenylalanine Phe – F 2.2 9.2
Tyrosine Tyr – Y 2.2 9.1 10.1
Tryptophan Trp – W 2.4 9.4
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44. α-Amino Acids Found in Proteins
Backbone of the amino acids is red, R-groups are black
reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @
themedicalbiochemistrypage.org
Imino Acids
Proline Pro – P 2.0 10.6
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45. The amino acids found in proteins have a common
stereochemistry
Optical Properties of the Amino Acids
Isomerism
• In organic chemistry, this stereochemistry is
referred to as L (for levo, meaning left).
• A tetrahedral carbon atom with 4 distinct
constituents is said to be chiral
• Chirality is the ability of a molecule to rotate
the plane of polarized light either to the right
(dextrorotatory) or to the left (levorotatory).
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46. • All of the amino acids in proteins exhibit the
same steric configuration as L-glyceraldehyde
• the amino group is always to the left side of the
alpha carbon, Thus, the amino acids found in
proteins are L-alpha amino acids
• D-amino acids are never found in proteins,
although they exist in nature. D-amino acids are
often found in polypetide antibiotics
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47. Acid-Base Properties of the Amino
Acids
• The α-COOH and α-NH2 groups in amino acids are
capable of ionizing (as are the acidic and basic R-
groups of the amino acids). As a result of their
ionizability the following ionic equilibrium
reactions may be written:
• R-COOH <——> R-COO– + H+
• R-NH3+ <——> R-NH2 + H+
• The equilibrium reactions, demonstrate that
amino acids contain at least two weakly acidic
groups.
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48. the carboxyl group is stronger acid than the amino group. At
physiological pH (around 7.4) the carboxyl group will be
unprotonated and the amino group will be protonated.
An amino acid with no ionizable R-group would be electrically
neutral at this pH. This species is termed a zwitterion.
An amino acid in its (1) un-ionized and (2) zwitterionic
forms
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49. • Carboxylic acid groups (−CO2H) can be
deprotonated to become negative
carboxylates (−CO2− ),
• and α-amino groups (NH2−) can be protonated
to become positive α-ammonium groups
(+NH3−).
•
•
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50. Amino acid and peptide linkage
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51. Peptide linkage
amino acids are the structural units of the body protein. They are
all α amino-carboxylic acids. All amino acids join together to
form Peptide link. Peptide bond is formed by condensation
reaction and broken by hydrolysis
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52. Peptide linkage
All peptides and polypeptides are polymers of α-
amino acids
• *A protein starts as a chain of amino acids,
called a polypeptide
• *Amino acids are joined by the peptide bond,
via dehydration synthesis to form the
polypeptide
• *The polypeptide chain is referred to as the
primary structure of the protein.
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53. • *The specific amino acids in the polypeptide
chain will determine its configuration, or
shape, and therefore, its function.
• one amino acid substitution in the bonding
sequence of a polypeptide can alter the final
protein's shape and ability to function
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54. Essential and non essential amino acids
Essential Nonessential
Isoleucine Alanine
Leucine Asparagine
Lysine Aspartic Acid
Methionine Cysteine*
Phenylalanine Glutamic Acid
Threonine Glutamine*
Tryptophan Glycine*
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55. Essential Nonessential
Valine Proline*
Selenocysteine*
Serine*
Tyrosine*
Arginine*
Histidine*
Ornithine*
Taurine*
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56. • *Nonessential amino acids can be synthesized
through a process called transamination.
• *Transamination involves the transfer of an
amino acid group from 1 amino acid to a
carbon skeleton to form a new amino acid.
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57. Dr. Siham Gritly 57

58. • Amino acids can be transaminated to form
alanine from pyruvate
• *the alanine is transported to the liver as
primary substrate for gluconeogenesis
• *this process known as glucose-alanine cycle
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59. Diseases associated with protein
Sickle Cell Compared
with Normal Red Blood Cell
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60. • sickle-cell anemia: a hereditary form of anemia
• characterized by abnormal sickle- or crescent-shaped
red blood cells. Sickled cells interfere with oxygen
transport and blood flow.
• Symptoms are precipitated by dehydration and
insufficient oxygen (as may occur at high altitudes) and
include hemolytic anemia (red blood cells burst), fever,
and severe pain in the joints and abdomen.
• gene expression: the process by which a cell converts
• the genetic code into RNA and protein.
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61. Protein-Energy Malnutrition
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62. • Adult Bone Loss (Osteoporosis
• Cancer
• Heart disease
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63. Protein synthesis
• *For synthesis of protein all amino acids should be
present or available at the same time (essential amino
acids). Synthesis or building of body proteins
controlled by genetic material found in every cell.
• *the genetic material found in the nucleus of the cell
is Deoxyribose Nucleic Acid (DNA)
• *the material DNA is used for synthesis of Ribose
Nucleic Acids (RNA).
• *there are different forms of RNA, such as mRNA
which carries information to the cytoplasm where the
protein are synthesized.
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64. • *DNA & RNA are composed of ribose
(pentose sugar) or deoxyribose, phosphoric
acid and nitrogenous base (purine and
pyrimidine)
• *in cytoplasma RNA moleculs tRNA direct the
amino acids to correct position with the mRNA
to built peptide chain and thus formation of
body proteins.
• The coming lectures the discussion will be in more details
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65. • This process of messenger RNA being made
from a template of DNA is known as
transcription.
• This process of messenger RNA directing the
sequence of amino acids and synthesis of
proteins is known as translation.
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66. Protein break down (catabolism)
• *any amounts above the needed amino acids
for synthesis of tissues are metabolized.
• *amino acids have both amino group and
carboxylic group. The amino group of amino
acid is converted to urea in the liver and
excreted in urine through urea cycle.
• *carboxylic group of amino acids are
converted to glucose and enter glycolysis
pathway for energy.
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67. Lab technique for studying protein purification,
structure and function
• Proteins may be purified from other cellular
components using a variety of techniques;
• such as ultracentrifugation,
• precipitation,
• electrophoresis, and chromatography;
• Methods commonly used to study protein structure and
function include; immunohistochemistry,
• site-directed mutagenesis,
• nuclear magnetic resonance
• mass spectrometry
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68. References
• Murry K. Robert, Granner K. daryl, Mayes A. peter, Rodwell
W. Victor (1999). Harpers Biochemistry. Appleton and Lange ,
twenty fifth edition
• Heymsfield, SB.; Olafson RP.; Kutner MH. and Nixon DW.
1979. A radiographic method of quantifying protein-calorie
under nutrition American Journal of Clinical Nutrition,
32: 693-702
• Chang, Raymond (2007). Chemistry, Ninth Edition. McGraw-
Hill. pp. 52.
• Sareen S. Gropper, Jack L.Smithh and James L. Groff; 2007.
advanced Nutrition and Human Metabolism, fifth ed.
Wadsworth CENGAGE learning
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69. • Michael W King, PhD | © 1996–2012 themedicalbiochemistrypage.org, LLC | info
@ themedicalbiochemistrypage.org
• D. Voet, J. G. Voet, Biochemistry, second edition ed., John Wiley &
• Sons, New York, 1995
• Sareen Gropper, Jack Smith and James Groff, Advanced Nutrition and Human
Metabolism, fifth ed. WADSWORTH
• Melvin H Williams 2010; Nutrition for Health, Fitness and Sport. 9th ed, McGraw
Hill
•
• Heymsfield, SB.; Baumgartner N.; Richard and Sheau-Fang P. 1999. Modern
Nutrition in Health and Disease; Shils E Maurice, Olson A. James, Shike
Moshe and Ross A. Catharine eds. 9th edition
• Guyton, C. Arthur. 1985. Textbook of Medical Physiology. 6th edition, W.B.
Company
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