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Introduction to Biochemistry

Assoc.Prof. Dr. Hasenan Nordin Dept. of Chemical Pathology USM Kubang Kerian Kelantan

Introduction
• In human and other vertebrate animals, the specialized cell groups include a gastrointestinal system to digest and absorb food; a respiratory system to take up O2 and eliminate CO2; a urinary system to remove wastes; a cardiovascular system to distribute nutrients, O2 and the products of metabolism; a reproductive system to perpetuate the species; and nervous and endocrine systems to coordinate and integrate the functions of the other systems.
• W.F Ganong

Cell
A cell is an intricate and complex structure where a lot of things constantly happen. For example, the cell structure needs to be constantly maintained, signals and materials need to be transferred in and out of the cell, energy must be harvested for use in e.g. physical and chemical work.

we need to understand how the different parts of the cell are constructed and how they interact with each other .Cont’d To understand how a cell works.

are also the main components of a cell. together with nucleic acids. compounds (food) are broken down into simpler constituents. fat (lipids). and protein.The main sources of both materials and energy are carbohydrates. . and the energy released is transported and used for synthesis of cellular components and for other types (e.g. physical) of work. These three classes of compounds. After ingestion.

and nucleic acids . proteins. lipids. properties. and cellular functions of carbohydrates.Cont’d The basic structure.

.Protein • Proteins are built up from amino acids which are linked by peptide bonds to form a polypeptide of defined sequence. Many proteins are folded into well defined globular shapes because the hydrophobic effect forces hydrophobic side chains along the polypeptide sequence to cluster together in a hydrophobic core.

Secondary (2°) structure. Tertiary (3°.Structure of protein Primary (1°) structure (the amino acid sequence). Quaternary (4°) structure in the case of multi-chain proteins . 3D) structure.

. Anabolic reactions require the input of energy. In anabolism. in which organic nutrient molecules are converted to smaller products. generally in the form of the free energy of hydrolysis of ATP and the reducing power of NADH and NADPH. also called biosynthesis. Catabolism is the degradation phase of metabolism.Metabolism • Metabolism is the sum of all of the chemical transformations that occur in a cell or organism. small molecules are used to make larger and more complex molecules.

How is it possible for the molecules to be transported into cells when the lipid bilayer is almost impermeable for most ions and molecules? .Membrane transport Ingested nutrients are digested and absorbed in the gastrointestinal tract and transported via the blood system to different organs for use as energy or as precursors for biosynthesis.

urea etc. . called transporters. Active transport is energy dependent and the transport is often connected to the hydrolysis of ATP as an energy source. Only small uncharged molecules such as water. This transport also occurs from higher to lower concentration without any need for energy input.Cont’d Accomplished by specific membrane proteins. Facilitated diffusion is transport of solutes through integral membrane proteins. can pass through the lipid bilayer by simple diffusion. Input of energy for transportation of solutes makes it possible to transport aqueous solutes against a concentration gradient.

Enzymes Macromolecules. usually proteins. by binding the needed reactants (substrates) in an active sites that is specific to the reaction to be carried out . that can catalyze (speed up) particular chemical reactions.

• There are numerous coenzymes which participate in metabolism. • NAD and NADP are the cofactors for large groups of dehydrogenases and reductases and participate in two-electron transfer reactions .Cofactors • Essential ions and coenzymes.

Kinases. one of which binds ATP and the other the substrate. a total of 2 ATP and 2 NADH are gained.Cont’d During the conversion of glucose to pyruvate via the glycolysis pathway. dehydrogenases and isomerases are important enzymes in the pathway. Kinases transfer a phosphate group to or from ATP. They consist of at least two domains. Phosphofructokinase is particularly important in the control of glycolysis . Conformational changes play an important role in the catalysis carried out by these enzymes.

Cont’d Many key enzymes in metabolism are allosterically regulated. . Phosphorylation of enzymes is a general way to regulate their activity. often through feed-back inhibition.

Vitamins are classified in two major groups: water soluble and fat soluble. One example is the enzyme complex named pyruvate dehydrogenase where four different vitamins are involved in the conversion of pyruvate to acetyl CoA .Vitamins • Vitamins are small biomolecules that are needed in small amounts in the diet. B-vitamins comprise a large group of vitamins which are involved in several different biochemical reactions.

with two monosaccharide units. . consist of a single polyhydroxy aldehyde or ketone unit. 3) Polysaccharides consist of long chains having hundreds or more of monosaccharides units. 2) Oligosaccharides consist of short chains of monosaccharide units joined together with glycoside linkages.Carbohydrates There are three major classes of carbohydrates: 1) Monosaccharides. The most abundant oligosaccharides are the disaccharides. or simple sugars.

There is a net gain of two ATP and 2 NADH per oxidized glucose. The process is catalysed by ten cytosolic enzymes. . and all of the intermediates are phosphorylated compounds.Glycolysis Metabolic pathway for the catabolic conversion of glucose to pyruvate with the formation of ATP.

Succinyl-CoA reacts with GDP and Pi to form free succinate and GTP. Succinate is then oxidised to fumarate by succinate dehydrogenase which is further oxidsed to malate by NAD-linked malate dehydrogenase to regenerate a molecule of oxaloacetate. Isocitrate is formed which is further oxidised to a-ketoglutarate by isocitrate dehydrogenase in a reaction that also yields CO2. .The citric acid cycle • The enzyme citrate synthase catalyses the condensation of acetyl CoA with oxaloacetate (a four carbon unit) to form citrate. a-ketoglutarate then undergoes dehydration and decarboxylation to succinylCoA and CO2.

fuel molecules. etc. Acetyl groups are translocated from mitochondria to the cytosol as citrate .Pentose phosphate pathway and fatty acid metabolism Fatty acids form phospholipids and glycolipids (components of cell membranes). Fatty acid synthesis requires C atoms (as acetyl CoA) and NADPH. precursors of hormones and intracellular messengers.

Hormones Hormones are chemical messengers synthesized by the body that initiate responses by high binding affinity and specificity to target cell receptors within the various organs in the body Simply defined as a chemical messenger from one cell ( or a group of cells) to another .

Function of hormones • • • • • Homeostasis Reproduction Growth and development Maintenance of internal environment Production. utilization and storage of energy .

steroid hormones.able to enter cell .Types of Hormones • Water-soluble – protein based hormone use secondary messenger • Fat soluble .

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Mechanisms: intrinsic to body fluids & cardiovascular system Osmotic movement of water across cell membranes buffers ECF osmolality Osmotic movement of water across capillary membranes buffers acute changes in plasma volume Venous compliance Glomerular Filtration .Water regulation Body fluid homeostasis: stability in the osmolality of body fluids & volume of plasma.

• Frequently encountered. • Life threatening when severe. • Needs monitoring and close follow up.Fluids and Electrolytes Imbalance • Common to all divisions in all departments and in all branches of medicine. . • Difficult to treat. frequently mismanaged.

The important buffer systems include proteins. via exhalation of carbon dioxide.Acid-Base Balance The normal pH of systemic arterial blood is 7. Of body fluids. . and via kidney excretion of H+ and reabsorption of HCO3. carbonic acid-bicarbonate buffers and phosphates.45. especially ECF.35-7. pH is maintained by buffers.. Homeostasis of pH is maintained by buffer systems. The overall acid-base balance is maintained by controlling the H+ conc.

a sugar.Nucleic Acids • Composition: Made up of nucleotides which each consist of three parts . and a phosphate group (from H3PO4) • Structure: polynucleotides which consist of bases attached to a backbone of sugar and phosphate groups . a base.

Cont’d • Nucleic acids are polymers of nucleotides • DNA and RNA: serve as the blueprints for proteins • They ultimately control the life of a cell .

DNA is double stranded: two polynucleotides twisted into a double helix • Consists of four types of nucleotides • Adenine pairs to Thymine • Cytosine pairs with Guanine – The sequence of nitrogenous bases carries genetic information Base pair Nitrogenous base (A) .

and ribosomal . C. and U • Unlike DNA. G. transfer. contains the base uracil in place of thymine • Three types of RNA that are key players in protein formation: messenger.RNA • Usually single strands • Four types of nucleotides: A.

Hiram F Gilbert • Review of Medical Physiology. Ganong . William F. Allan D Marks. Colleen M Smith • Basic Concepts in Biochemistry. Dawn B Marks. A Clinical Approach.References • Basic Medical Biochemistry.