Biochemistry

for Nursing Students CHS 262

Biochemistry CHS 262

This course Prepared by

Dr.Eman Saqr

2

Course Directors

***********

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

Introduction

This course aims to enhance the study of

general and basics of Biochemistry for nursing

students.

•Biochemistry is the language of biology.

• The tools for research in all the branches of

medical science are mainly biochemical in

nature.

The study of biochemistry is essential to

understand:

Biomolecules.

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.

Recommended Books, References &

Teaching Materials

•Biochemistry by P.C. Champe, R.A. Harvey and

D.R. Ferrier 3rd Edition 2005 Lippincott’s

Illustrated Reviews

•Textbook of biochemistry for dental students by

DM Vasudevan, Sreekumari S and Kannan

Vaidyanathan, 2nd Edition 2011.

•Handbook of biochemistry (For allied and

nursing students) by Shivananda Nayak B 1st

Edition 2007.

Teaching Methodology: • Lecture. 2hours •Practical Session. 2hours

Assessment Tools: 20% Mid term-Exam 20% Assignments 20% Practical 40% Final Exam

Assignments are:

• 5 marks for each of Research project, Oral, and Quizzes.

• 5 marks for attendance, attitude and participation during lecture session.

Lectures schedule 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

Biochemistry, 3rd Edition 2005

Lippincott’s Illustrated Reviews

Unit I/ Chapter 1 pp. 1-12

3 9/2/2013

Structure of proteins.

Unit I/ Chapter 2 pp. 13-24

4 16/2/2013 Nitrogen metabolism.

Unit IV/ Chapter 19 pp. 245-260 Quiz 1

5 23/2/2013

Enzymes. Unit I/ Chapter 5 pp. 53-68

6 2/3/2013

Introduction to

carbohydrates and

Glycolysis

Unit II/ Chapter 7, 8 pp. 83-108 Quiz 2

7 9/3/2013

Mid Term Exam

8 16/3/2013

Tricarboxylic acid cycle and Gluconeogenesis.

Unit II/ Chapter 9, 10 pp. 109-124

9

23/3/2013

Mid Term Vacation

10 30/3/2013

Glycogen metabolism Unit II/ Chapter 11 pp. 125-136

11 6/4/2013

Metabolism of dietary lipids

Unit III/ Chapter 15 pp.173-180

12 13/4/2013

Fatty acid and triacylglycerol metabolism.

Unit III/ Chapter 16 pp. 181-200

Quiz 3

13 20/4/2013

Water soluble vitamins

Unit V/ Chapter 27 pp. 373-381

14 27/4/2013 Fat soluble vitamins Unit V/ Chapter 27 pp.

381-394

15 6/5/2013

Gene expression and protein synthesis

Unit VI/ Chapter 31 pp.431-448

Quiz 4

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

Project

• Each one can choose one diseases 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.

Female-TableTime Course Time

Tuesday

Theoretical 8-10

Class

Practical Tuesday

10-12

Office Hours Tuesday

12-2

Male-TableTime Course Time

Wednesday

Theoretical 6-8

Class

Practical Wednesday

8-10

Office Hours Saturday

7-9

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.

Protein • Proteins are the most abundant and functionally diverse

molecules in living systems.

• Virtually every life process depends on this class of

molecules. For example, enzymes and polypeptide

hormones direct and regulate metabolism in the body,

whereas contractile proteins in muscle permit movement.

• 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.

Amino acids Although more than 300 amino acids have

been described in nature, only 20 are

commonly found as constituents of

mammalian proteins

• 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.

• At physiologic pH (7.4), the carboxyl group is

dissociated, forming the negatively charged

carboxylate ion (-coo-), and the amino group is

protonated (-NH3+).

• Thus, it is the nature of the side chains that

ultimately dictates the role an amino acid plays in a

protein.

Classification of amino acids

• According to the properties of their side chains, that is, whether they are:

A. Nonpolar, have an even distribution of electrons.

B. Polar, have an uneven distribution of electrons, such as acids and bases.

A. Amino acids with nonpolar side chains

• These groups are hydrophobic and lipophilic.

• Each of these amino acids has a nonpolar

side chain that does not gain or lose protons

or participate in hydrogen or ionic bonds.

• As, Glycine, Alanine, Valine, Leucine,

Isoleucine, Phenylalanine, Tryptophan,

Methionine, Proline.

• The side chains of these amino acids can be

thought of as ‘oily’ or lipid-like,

Location of nonpolar amino acids in proteins:

• In proteins found in aqueous solutions- a polar environment- the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein.

• The nonpolar R-groups thus fill up the interior of the folded protein and help give it its three dimensional shape.

• However, for protein that are located in a hydrophobic environment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid environment (F. 1.4).

Proline:

• Proline differs from other amino acids in that

proline’s side chain and α-amino N form a rigid,

five-membered ring structure (F 1.5).

• It is frequently referred to as imino acid.

• The unique geometry of proline contributes to the

formation of the fibrous structure of collagen,

and often interrupts the α-helices found in

globular proteins.

B. Amino acids with uncharged polar

side chains

• These groups are hydrophilic in nature.

• As, Serine, Threonine, Tyrosine, Asparagine, glutamine, Cysteine.

• These amino acids have zero net charge at neutral pH.

• Serine, Threonine and Tyrosine each contain a polar Hydroxyl group that can precipitated in hydrogen bond formation.

• The side chain of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds.

2. Side chains as sites of attachment

for other compounds:

• Polar hydroxyl group of serine, threonine,

and rarely, tyrosine, can serve as a site of

attachment for structures such as a

phosphate group.

• In addition, the amide group of asparagine,

as well as the hydroxyl group a serine or

threonine, can serve as a site of attachment

for oligosaccharide chains in glycoproteins.

C. Amino acids with acidic chains

• These groups are hydrophilic in nature.

• The amino acids aspartic and glutamic acid are

proton donors.

• At physiologic pH, the side chains of these

amino acids are fully ionized, containing a

negatively charged carboxylate group (-COO-).

• They are, therefore, called aspartate or

glutamate to emphasize that these amino acids

are negatively charged at physiologic pH.

D. Amino acids with basic side chains

• These groups are hydrophilic in nature.

• The side chains with basic amino acids accept

protons.

• Ex., arginine, lysine, histidine.

• However, when histidine is incorporated into a

protein, its side chain can be either positively

charged or neutral.

• This is an important property of histidine that

contributes to the role it plays in the functioning of

proteins such as hemoglobin.

Amino acids with basic chains

Abbreviations and symbols for

commonly occurring amino acids

• Each amino acid name has an associated three-letter

abbreviation and a one-letter symbol.

• The one-letter codes are determined by the

following rules:

1. Unique first letter:

If only one amino acid begins with particular letter,

then that letter is used as its symbol.

For example, I = isoleucine.

2. Most commonly occurring amino acids have priority:

If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbol.

For example, glycine is more common than glutamate, so G = glycine.

3. Similar sounding names:

Some one-letter symbol sound like the amino acid they represent.

For example, F= phenylalanine, or

W = tryptophan

4. Letter close to initial letter:

For the remaining amino acids, a one-letter symbol

is assigned that is as close in the alphabet as possible

to the initial letter of the amino acid, for example,

K= lysine

B is assigned to Asx, signifying either aspartic acid

or asparagine.

Z is assigned to Glx, signifying either glutamic

acid or glutamate.

X is assigned to an unidentified amino acid.

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.

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.

Physical properties of amino acids

Optical properties

• 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.

Acidic and basic properties of amino

acids

• Amino acids in aqueous solution contain weakly

acidic α-carboxyl groups and weakly basic α-

amino groups.

• In addition, each of the acidic and basic amino

acids contains an ionizable group in its side chain.

• Thus, both free amino acids and some amino

acids combined in peptide linkages can act as

buffers.

B. Buffers

• A buffer is a solution that resist change in pH

following the addition of an acid or base.

• In biochemistry: An ionic compound that

when added to a solution neutralizes both acids

and bases without significantly changing the

original acidity or alkalinity of a solution

• Buffer capacity:

It is the ability of the buffer to resist changes in pH

when an acid or base is added.

Acid-Base balance • Normal pH:

• The pH of plasma is 7.4 in normal life, the variation of plasma pH is very small. The pH of plasma is maintained within a narrow range of 7.38 to 7.42. The pH of the interstitial fluid is generally 0.5 units blow that of the plasma.

• Acidosis: • If the pH is blow 7.38, it is called acidosis. Life is

threatened when pH is lowered below 7.25. Death occurs when pH is below 7.

• Alkalosis: • When the pH is more than 7.42, it is alkalosis. It is very

dangerous if pH is increased above 7.55. Death occurs when the pH is above 7.6.