Biochemistry CHS 262 This course Prepared by Dr.Eman Saqr Course Directors ***********Associate Prof. Dr. Ehab(Male)Assistant Prof.Dr. Eman Saqr (Female)2
IntroductionThis 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 ofmedical science are mainly biochemical innature.
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 andD.R. Ferrier 3rd Edition 2005 Lippincott’sIllustrated Reviews•Textbook of biochemistry for dental students byDM Vasudevan, Sreekumari S and KannanVaidyanathan, 2nd Edition 2011.•Handbook of biochemistry (For allied andnursing students) by Shivananda Nayak B 1stEdition 2007.
Teaching Methodology:• Lecture. 2hours•Practical Session. 2hoursAssessment Tools: 20% Mid term-Exam 20% Assignments 20% Practical 40% Final ExamAssignments are:• 5 marks for each of Research project, Oral, and Quizzes.• 5 marks for attendance, attitude and participation during lecture session.
Lectures scheduleWeek Date/Saturday Subject Reading assignment Quizzes 1 26/1/2013 Registration Introduction of Biochemistry, 3rd Edition 2005 biochemistry and Lippincott’s Illustrated Reviews 2 2/2/2013 explain the course syllabus Amino acids Unit I/ Chapter 1 pp. 1-12 9/2/2013 3 Structure of proteins. Unit I/ Chapter 2 pp. 13-24 Nitrogen metabolism. Unit IV/ Chapter 19 pp. 245-260 Quiz 1 4 16/2/2013 23/2/2013 Enzymes. Unit I/ Chapter 5 pp. 53-68 5 Introduction to Unit II/ Chapter 7, 8 pp. 83-108 Quiz 2 6 2/3/2013 carbohydrates and Glycolysis 9/3/2013 7 Mid Term Exam Tricarboxylic acid cycle Unit II/ Chapter 9, 10 pp. 109-124 16/3/2013 and Gluconeogenesis. 8 9 23/3/2013 Mid Term Vacation
Glycogen metabolism Unit II/ Chapter 11 pp. 125-13610 30/3/2013 Metabolism of dietary Unit III/ Chapter 15 lipids pp.173-18011 6/4/2013 13/4/2013 Fatty acid and Unit III/ Chapter 16 Quiz 312 triacylglycerol pp. 181-200 metabolism. 20/4/2013 Water soluble Unit V/ Chapter 27 pp.13 vitamins 373-381 Fat soluble vitamins Unit V/ Chapter 27 pp.14 27/4/2013 381-394 Gene expression Unit VI/ Chapter 31 Quiz 415 6/5/2013 and protein synthesis pp.431-448 13/5/2013 Practical Exam1617 20/5/2013 Oral Exam 27/5/201318 1/6/2013 Final Exam19 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.
Time Table-FemaleCourse Time TuesdayTheoretical 8-10 ClassPractical Tuesday 10-12Office Hours Tuesday 12-2
Time Table-MaleCourse Time WednesdayTheoretical 6-8 ClassPractical Wednesday 8-10Office 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 acidsAlthough 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 attachmentfor 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.
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 havepriority: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 acidor asparagine. Z is assigned to Glx, signifying either glutamicacid or glutamate. X is assigned to an unidentified amino acid.
Classification according to nutritional requirement1- 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 theoriginal acidity or alkalinity of a solution• Buffer capacity:It is the ability of the buffer to resist changes in pHwhen 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.