Biochemistry for Dental Students

1. Biochemistry 1
for Dental Students
BCH 261

2. Biochemistry BCH 261
This course Prepared by
Dr.Eman Saqr
2
Course Directors
***********
Associate Prof. Dr. Ehab(Male)
Assistant Prof.Dr. Eman Saqr (Female)

3. Course Objectives
To give the dental student the basic
knowledge of biochemistry which
is related to dentistry and
medicine.
3

4. The study of biochemistry is essential
to understand:
Basic functions of the body.
How the food that we eat is digested, absorbed, and used
to make ingredients of the body?
How does the body derive energy for normal day to day
work?
How are the various metabolic processes interrelated?
What is the function of genes?
The study of biochemistry is necessary to give the
scientific basis for disease and is useful for intelligent
treatment of patients.
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5. Lectures schedule-Male/Female
Week Date/Saturday Subject
Reading
assignment
Quizzes
1
26/1/2013
Registration
2 2/2/2013
Introduction of
biochemistry and
explain the course
syllabus
Amino acids
Text book of
Biochemistry for
Dental Students 2th
edition
Chapter 2 pp. 7-12
3
9/2/2013 A Chemistry of
Proteins
Chapter 2 pp. 12-18
4 16/2/2013
Protein metabolism Chapter 12 pp. 107-109 Quiz 1 in the time of
practical session
5
23/2/2013
- urea cycle
- Introduction to
enzyme
Chapter 12 pp. 110-111
Chapter 3 pp. 19-22
6 2/3/2013
Enzymes and coenzyme Chapter 3 pp. 23-29 Quiz 2 in the time of
practical session
7
9/3/2013
Chemistry and
digestion of
carbohydrates
Chapter 4 pp. 31-41
5

6. 10 30/3/2013
Carbohydrate
metabolism I
[Glycolysis, citric acid
cycle and
gluconeogenesis]
Chapter 5 pp. 42-50
Chapter 14 pp. 128-132
11 6/4/2013
Carbohydrate
metabolism II
[Glycogen metabolism
and pentose shunt]
Chapter 5 pp. 50-53
Chapter 7 pp. 61-62
12
13/4/2013 Chemistry of lipids Chapter 9 pp. 76-82 Quiz 3 in the time of
practical session
13
20/4/2013 Lipid metabolism. Chapter 10 pp. 83-95
14 27/4/2013
DNA: Structure and
replication
Chapter 24 pp. 209-214 Quiz 4 in the time of
practical session
15 6/5/2013
Genetic code and
Protein biosynthesis
Chapter 25 pp. 215-221
16 13/5/2013 Practical Exam
17
20/5/2013 Oral Exam
18
27/5/2013
Final Exam
19
1/6/2013
5/6/2013
Summer Vacation
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7. Recommended Books, References &
Teaching Materials
•Textbook of biochemistry for dental students by DM
Vasudevan, Sreekumari S and Kannan
Vaidyanathan, 2nd Edition 2011.
•Biochemistry by P.C. Champe, R.A. Harvey and D.R.
Ferrier 3rd Edition 2005 Lippincott’s Illustrated Reviews
•Handbook of biochemistry (For allied and nursing
students) by Shivananda Nayak B 1st Edition 2007.
7

8. Teaching Methodology:
• Lecture. 1hours
•Practical Sessions. 2 hours
Assessment Tools for each semester:
20% - Mid-Exam
40% - Final Exam
20% - Assignments
20% - Practical
Assignments are:
• 5 marks for each of Research project, Oral, and
Quizzes.
• 5 marks for attendance, attitude and participation
during lecture session.
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9. Research Project
• Each one can choose one type of enzyme as
a subject of the project.
• Five students from each group will discuss
their project weekly starting from the third
week according to their presence in the
attendance sheet.
• The only excuse is by recommended medical
certificate.
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10. Time Table for Female
Group One Group Two
Theoretical
Sunday Sunday
11-12 8-9
Class 17 Class 11
Practical
Sunday Sunday
12-2 9-11
Office Hours Saturday 10-12
10

11. Time Table for Male
Group One Group Two
Theoretical
Sunday Sunday
7-8 4-5
Class 15 Class 15
Practical
Sunday Sunday
8-10 5-7
Office Hours Saturday 5-7
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12. Biomolecules
 The human body is composed of 6 elements, oxygen,
carbon, hydrogen, nitrogen, calcium and phosphorus.
 Human body is composed of about 60% water, 15%
proteins, 15% lipids, 2% carbohydrates and 8% minerals.
 Biomolecules are covalently linked to each other to form
macromolecules of the cell, eg. Glucose to glycogen and
amino acids to proteins.
 Major complex biomolecules are proteins,
polysaccharides, lipids and nucleic acids.
 The macromolecules associate with each other to form
supramolecular systems, e.g. ribosomes, lipoproteins.
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13. Protein
Definition:
• Proteins are group of organic compounds
composed of carbons, hydrogen, oxygen and
nitrogen (sulphur and phosphorus may also
present).
• They are the most important of all biologic
substances .
• They are polymers of L-amino acids linked
together by peptide bonds.
13

14. Amino acids
Definition:
• They are the building blocks of proteins.
• They are organic compounds, which contain two
functional groups, amino group (-NH2) and
carboxyl group (-COOH).
• The amino group is usually attached to the α-
carbon atom (next to the -COOH group).
• Amino acids present in proteins are of the α-L-type
i.e. the amino (H2N-) group is present on the left
side of the vertical formula.
14

15. 15

16. Classifications of amino acids
• Classification according to structure
• Classification according to side chain
• Classification according to metabolic fate
• Classification according to nutritional requirement
•
16

17. Classification according to structure
1- Aliphatic aminoacids:
a. Mono amino mono carboxylic acids
• Simple amino acids (Glycine Gly, Alanine Ala)
• Branched chain a.a. (Valine Val, Leucine Leu, Isoleucine
Ile)
• Hydroxy a.a. (Serine Ser, Threonine Thr)
• Sulphur containing a.a. (Cysteine Cys, Methionine Met)
• Having amide group (Asparagine Asn, Glutamine Gln)
b. Mono amino dicarboxylic acids
Aspartic acid Asp, Glutamic acid Glu
c. Dibasic mono carboxylic acids
Lysine Lys, Arginine Arg
17

18. 18

19. 2- Aromatic amino acids:
• Phenylalanine Phe, Tyrosine Tyr
3- Heterocyclic amino acids:
• Tryptophan Trp, Histidine His
4- Imino acid
• Proline Pro
19

20. 5- Derived amino acid
• Derived amino acids found in protein. Some
amino acids modified after protein synthesis
such as hydroxy proline and hydroxy lysine which
are important component of collagen. Gamma
crboxylation of glutamic acid residues of proteins
is important for clotting process.
• Derived amino acids not seen in protein. Some
derived amino acids are seen free in cells as
ornithine. Others produced during the
metabolism of amino acids as citrulline and
homocysteine. All of these amino acids called
Non-protein amino acids.
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21. Classification according to side chain
1- Amino acids having nonpolar side chain:
• These groups are hydrophobic and lipophilic.
• These include, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline,
Phenylalanine and Tryptophan.
2- Amino acids having uncharged or nonionic polar side chain:
• These groups are hydrophilic in nature.
• These include, Glycine, Serine, Threonine, Cysteine, Tyrosine, Glutamine
and Asparagine.
3- Amino acids having charged or ionic polar side chain:
• These groups are hydrophilic in nature.
• Acidic amino acids: They have a negative charge on the R group include,
Aspartic acid and Glutamic acid (Tyrosine is midly acidic).
• Basic amino acids: They have a positive charge on the R group include,
Lysine, Arginine and Histidine.
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22. Classification according to metabolic
fate1- Purely Ketogenic:
• Leucine is purely ketogenic because it will enter into the
metabolic pathway of ketogenesis.
2- Ketogenic and Glucogenic:
• Lysine, Isoleucine, Phenylalanine, Tyrosine and Tryptophan are
partially ketogenic and partially glucogenic.
• During metabolism, part of the carbon skeleton of these amino
acids will enter the fatty acid metabolic pathway and the other
part into glucose pathway.
3- Purely Glucogenic:
• All the remaining 14 amino acids are purely glucogenic as they
enter only into the glucogenic pathway.
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23. Classification according to nutritional
requirement
1- Essential or indispensable:
• These groups are essential for growth.
• Their carbon skeleton of these amino acids
cannot be synthesized by human being.
• These include, Isoleucine, Leucine, Threonine,
Lysine, Methionine, Phenylalanine,
Tryptophan and Valine.
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24. 2- Partially essential or semi-essential:
• Growing children require them in food, but they
are not essential for the adult individual.
• These include, Histidine and Arginine.
2- Nonessential or dispensable:
• The remaining 10 amino acids are nonessential.
• They also required for normal protein synthesis.
• Their carbon skeleton can be synthesized by
metabolic pathways.
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25. Properties of amino acids:
I. Physical properties
1- .Amphoteric properties:
• _ In solution, amino acids behave as acids and alkalis due
to the presence of acidic group (-COOH) and basic group
(-NH2). On complete ionization of neutral amino acids it
acts as dipolar ions (Zwitterions or hybrid), they carry both
negative and positive charges, which are equal. This
explains the amphoteric
• property of amino acid, i.e. they can react with acids and
bases.
• At isoelectric point, the amino acid carry no net charge; all
the groups are ionized but the charges will cancel each
other. Therefore, at iso-electric points, there is no mobility
in an electrical field. Also solubility and buffering capacity
will be minimum.
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26. 2- Optical activity ;
• _ All amino acids except glycine are optically
active. Each optically active amino acid contains
one asymmetric α-C atom attached to four
different groups.
• They occur in D and L forms.
• The naturally occurring amino acids in proteins
are of the L-α amino acid form.
• D-amino acids are found in some antibiotics and
bacteria.
26

27. 27

28. II. Chemical properties
1- Reactions due to carboxyl group:
A. Decarboxylation
• The amino acids will undergo alpha decarboxylation to
form the corresponding amine.
• Ex. Histidine ---------- Histamine +CO2
Tyrosine ---------- Tyramine +CO2
Tryptophan------- Tryptamine +CO2
Glutamic acid --- Gamma aminobutyric acid +CO2
28

29. Decarboxylation reaction
COOH
I
CH - NH2 ------------→ CH – NH2 + CO2
I I
R R
Amino acid Corresponding
amine
29

30. B. Amide formation:
• The –COOH group of dicarboxylic acids (other
than alpha carboxyl) can combine with ammonia
to form the corresponding amide.
• Ex. Aspartic acid + NH3 ------- Asparagine
Glutamic acid + NH3 ------- Glutamine
• These amides are components of protein
structure.
• The amide group of glutamine serves as the
source of nitrogen for nucleic acid synthesis.
30

31. Amide formation
31

32. 2- Reactions due to amino group
A.Transamination
• The alpha amino group of amino acid can be
transferred to alpha keto acid to form the
corresponding new amino acid and alpha keto
acid.
• This is an important reaction in the body for the
inter conversion of amino acids and for synthesis
of nonessential amino acids.32

33. Transamination reaction
33

34. B. Oxidative deamination
• The alpha amino group is removed from
the amino acid to form the corresponding
keto acid and ammonia.
• In the body, Glutamic acid is the most
common amino acid to undergo oxidative
deamination.
34

35. Oxidative deamination
35

36. Reaction due to amino group
Transamination and oxidative deamination
36

37. 3- Reactions due to side chains:
A. Ester formation by OH group
• The hydroxyl amino acids can form esters with
phosphoric acid.
• In this manner the Serine and Threonine
residues of proteins are involved in the
formation of phosphoproteins.
• Similarly these hydroxyl groups can form O-
glycosidic bonds with carbohydrate residues to
form glycoproteins.
37

38. B. Reaction of the amide group
The amide groups of Glutamine and Asparagine can
form N-glycosidic bonds with carbohydrate residues
to form glycoproteins.
C. Reactions of SH group
• Cysteine has a sulfhydryl (SH) group and it can form
a disulphide (S-S) bond with another Cysteine
residue.
• The two Cysteine residues can connect to
polypeptide chains by the formation of inter-chain
disulfide bonds or link.
• The dimer formed by two Cysteine residues is called
Dicysteine or cystine.38

39. Reactions of SH group
39

40. 4- Special functions of amino acids:
• Gamma aminobutyric acid (GABA), a derivative
of glutamic acid) and dopamine (derived from
tyrosine) are neuro-transmitters.
• Histamine (synthesized from histidine) is the
mediator of allergic reactions.
• Thyroxine (from tyrosine) is an important
thyroid hormone.
40

41. 5- Peptide bond:
• Alpha carboxyl group of one amino acid reacts
with alpha amino group of another amino acid to
form a peptide bond or CO-NH bridge. Proteins
are made by polymerization of amino acids
through peptide bonds.
• Two amino acids combined to form dipeptide.
Three amino acids form tripeptide. Four will
make a tetrapeptide.
41

42. 42

43. 43

44. 44

45. • A few amino acids together will make an
oligopeptide. Combination of 10 to 50 amino acids
is called a polypeptide.
• Big polypeptide chains containing more than 50
amino acids are called proteins.
• Acid hydrolysis (hydrochloric acid at higher
temperature) of peptides bonds will break the
proteins into amino acids. But hydrochloric acid at
body temperature will not break the peptide bonds.
• Thus in the stomach, HCL alone will not be able to
digest proteins; it needs enzymes.
45