Biochemistry 1 for Dental Students

BCH 261

Biochemistry BCH 261

This course Prepared by

Dr.Eman Saqr

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Course Directors

***********

Associate Prof. Dr. Ehab(Male) Assistant Prof.Dr. Eman Saqr (Female)

Course Objectives

To give the dental student the basic

knowledge of biochemistry which

is related to dentistry and

medicine.

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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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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

8 16/3/2013

Mid Term Exam

All questions are short notes

9 23/3/2013

Mid Term Vacation

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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 6

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.

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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. 8

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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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

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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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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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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.

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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.

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Classifications of amino acids

• Classification according to structure

• Classification according to side chain

• Classification according to metabolic fate

• Classification according to nutritional requirement

•

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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

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2- Aromatic amino acids:

• Phenylalanine Phe, Tyrosine Tyr

3- Heterocyclic amino acids:

• Tryptophan Trp, Histidine His

4- Imino acid

• Proline Pro

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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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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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Classification according to metabolic fate

1- 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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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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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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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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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.

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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

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Decarboxylation reaction

COOH

I

CH - NH2 ------------→ CH – NH2 + CO2

I I

R R

Amino acid Corresponding

amine

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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.

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Amide formation

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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.

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Transamination reaction

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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.

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Oxidative deamination

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Reaction due to amino group

Transamination and oxidative deamination

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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.

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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.

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Reactions of SH group

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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.

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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.

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• 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.

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