Introduction to Biochemistry

• Biochemistry studies the chemistry of biological organisms, bridging biology and chemistry.
• It explores chemical reactions and structures that underpin life processes.
• Biochemistry deals with biological macromolecules like proteins, nucleic acids, carbohydrates, and lipids.
• These macromolecules provide structure to cells and perform life's functions.
• Cellular chemistry relies on reactions of small molecules and ions, both inorganic and organic.
• Metabolism encompasses the chemical reactions cells use to harness energy from their environment.

Applications of Biochemistry

• Medicine: Investigates causes and cures of diseases.
• Nutrition: Focuses on maintaining health, wellness, and understanding nutritional deficiencies.
• Agriculture: Studies soil, fertilizers, crop improvement, storage, and pest control.

Carbohydrates

• Carbohydrates are biomolecules with carbon, hydrogen, and oxygen atoms.
• The hydrogen-oxygen atom ratio is typically 2:1, similar to water.
• The empirical formula is commonly written as Cm(H2O)n, though m can differ from n.
• They are the most abundant organic compounds in living organisms.
• Carbohydrates originate as products of photosynthesis.
• Photosynthesis is an endothermic reductive condensation of carbon dioxide, requiring light energy and chlorophyll.
• The general equation is n CO2 + n H2O + energy -> CnH2nOn + n O2.

Carbohydrate Classification

• Monosaccharides: Simple sugars with one sugar molecule (e.g., glucose, fructose, galactose).
• Disaccharides: Sugars with two sugar molecules (e.g., sucrose, lactose, maltose).
• Oligosaccharides: Sugars with two to ten sugar molecules (e.g., raffinose, stachyose).
• Polysaccharides: Complex carbohydrates with ten or more sugar molecules (e.g., starch, glycogen, cellulose).
• The formula of many carbohydrates can be written as carbon hydrates, Cn(H2O)n.
• Carbohydrates are a major source of metabolic energy for plants and animals.
• Aside from energy, carbohydrates serve as structural materials.
• Examples of structural roles is cellulose in plants.
• Carbohydrates are components of energy carriers like ATP and recognition sites on cell surfaces.
• They are also essential components of DNA and RNA.
• Carbohydrates are also called saccharides or sugars, especially the smaller ones.

Carbohydrate Complexity and Function

• Simple carbohydrates are monosaccharides.
• Complex carbohydrates include disaccharides, polysaccharides, and oligosaccharides.
• Tetrose sugars have 4 carbons.
• Pentose sugars have 5 carbons.
• Hexose sugars have 6 carbons.
• Heptose sugars have 7 carbons.
• Aldose sugars have an aldehyde group e.g., glucose.
• Ketose sugars have a ketone group e.g., fructose.
• Reducing sugars can be oxidized by Tollen's reagent.
• Non-reducing sugars cannot be oxidized by Tollen's reagent.

Glucose Structure and Reactions

• Glucose (C6H12O6) is a common carbohydrate example.
• Glucose is a monosaccharide.
• Glucose is an aldohexose (combining function and size classifications).
• Glucose is a reducing sugar.

Key Reactions of Glucose

• Hot hydriodic acid (HI) can reductively remove oxygen functional groups, yielding hexane from glucose.
• This indicates that the six carbons are in an unbranched chain.
• Cyanohydrin formation indicates an aldehyde carbonyl group.
• Reduction to sorbitol confirms the carbonyl group.
• Mild oxidation to glucuronic acid also indicates an aldehyde.
• Stronger oxidation by dilute nitric acid yields glucaric acid, supporting the six-carbon chain.
• The five remaining oxygens were thought to be in hydroxyl groups.
• A penta-acetate derivative can be made.
• Hydroxyl groups are assigned to the last five carbon atoms.
• Geminal hydroxyl groups are normally unstable.
• Glucose and other saccharides are cleaved by periodic acid (Malaprade reaction).
• Useful for analyzing selective O-substituted derivatives of saccharides.

Sugar classification

• Sugars are sweet crystalline substances soluble in water.
• Sugars are further classified based on their behavior on hydrolysis.
• Monosaccharides are colorless, crystalline solids freely soluble in water but insoluble in nonpolar solvents.
• Most monosaccharides have a sweet taste and unbranched carbon chains.
• One carbon atom is double-bonded to oxygen to form a carbonyl group; the others have hydroxyl groups.
• If the carbonyl group is at the end of the chain, it is an aldose (aldehyde).
• If the carbonyl group is at any other position, it is a ketose (ketone).
• The simplest monosaccharides are the two three-carbon trioses which are glyceraldehyde, an aldotriose, and dihydroxyacetone, a ketotriose.
• Monosaccharides with four, five, six, and seven carbon atoms are tetroses, pentoses, hexoses, and heptoses, respectively.
• D-glucose is an aldohexose
• D-fructose, is a ketohexose.
• D-ribose is an aldopentose
• 2-deoxy-D-ribose.

Disaccharides

• Disaccharides such as maltose, lactose, and sucrose consist of two monosaccharides joined by an O-glycosidic bond.
• The bond is formed when a hydroxyl group of one sugar molecule reacts with the anomeric carbon of the other.
• The resulting compound is called a glycoside.
• Glycosidic bonds are hydrolyzed by acid but resist cleavage by base.
• Disaccharides can be hydrolyzed to yield their free monosaccharide components by boiling with dilute acid.
• N-glycosyl bonds join the anomeric carbon of a sugar to a nitrogen atom in glycoproteins and nucleotides.
• Oligosaccharides generate 2 to 10 molecules of monosaccharides upon hydrolysis.
• An oligosaccharide yielding 2 molecules of monosaccharide on hydrolysis is designated as a disaccharide.
• General disaccharide formula: Cn(H2O)n-1.
• Trisaccharides yield 3 molecules of monosaccharide.
• General trisaccharide formula: Cn(H2O)n-2.
• Examples: Sucrose, Lactose, Maltose, Cellobiose, Trehalose, Gentiobiose, Melibiose (Disaccharides); Rhamninose, Gentianose, Raffinose, Rabinose, Melezitose (Trisaccharides), and Stachyose, Scorodose (Tetrasaccharides).

Polysaccharides

• Polysaccharides yield more than 10 molecules of monosaccharides on hydrolysis.
• Classified as homopolysaccharides or heteropolysaccharides.
• Homopolysaccharides yield the same type of monosaccharide.
• Heteropolysaccharides yield different types of monosaccharides.
• General Formula is (C6H10O5)x.
• Homopolysaccharide examples: Starch, Glycogen, Inulin, Cellulose, Pectin, Chitin.
• Heteropolysaccharide examples: "Specific soluble sugar" of pneumococcus typeIII, Hyaluronic acid, Chondroitin.

Examples of Polysaccharides

• Glycogen is the storage form of glucose in humans and other vertebrates.
• Glycogen is a highly branched molecule stored in liver and muscle cells.
• Glycogenolysis is the process of glycogen breakdown to release glucose.
• Cellulose is the most abundant natural biopolymer.
• The cell wall of plants is mostly cellulose.
• Cellulose provides structural support to the cell
• Wood and paper are mostly cellulosic.
• Cellulose comprises glucose monomers linked by β 1-4 glycosidic bonds.
• Every other glucose monomer is flipped over. This gives cellulose its rigidity. Mammals cannot digest cellulose.

Carbohydrate Diversity

• Different monosaccharides can be joined through any of several OH groups.
• The C-1 linkage can have alpha or beta configurations, and extensive branching is possible.

Tests for Sugars

• Benedict's Test for Sugars detects monosaccharides and disaccharides by classifying them as reducing or non-reducing.
• Reducing sugars include all monosaccharides and some disaccharides and are detected by Benedict's reagent (blue colour).
• A positive test forms a coloured precipitate when heated.
• Higher concentrations of reducing sugar produce a more intense colour change.
• Non-reducing sugars like sucrose must be broken down into monosaccharides first.
• Take a fresh sample and heat it with diluted hydrochloric acid or hydrolyze using enzymes. You can nNeutralize it with sodium hydrogen carbonate.
• Iodine Test for Starch detects starch. Add iodine dissolved in potassium iodide solution to the test sample.
• If starch is present, the sample changes from brown-orange to a dark blue-black colour.

Functions of Carbohydrates

• Provides energy and regulation of blood glucose.
• Prevents degradation of skeletal muscle and other tissues.
• Prevents breakdown of proteins for energy.
• Helps with fat metabolism as extra energy gets stored as fat.
• Important component of industries like textile, paper, lacquers, and breweries.
• Detoxification of physiological importance is carried out in some extent with carbohydrate derivatives.
• Agar is polysaccharide used in culture media, laxative and food.
• Carbohydrates form genetic material like DNA and RNA.
• Hyaluronic acid found supports frictionless movement.
• Helps make up the body mass by being included in all parts of the cell and tissues.
• Adequate storage of hepatic glycogen helps detoxifying a normal liver.
• Form components of bio molecules.
• Main fibre of diet better digestion.
• Help clear gut and prevent constipation.
• Source of fuel stored in plants.
• Provides sweetness to foods.

Saccharides

• Term commonly used in biochemistry.
• Saccharides are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides
• Ethanol fermentation, also called alcoholic fermentation
• It converts sugars into cellular energy, producing ethanol and carbon dioxide as by-products.
• Yeasts perform this conversion in the absence of oxygen which is anaerobic process.

Metabolism of Carbohydrates

• Carbohydrate metabolism is biochemical processes for metabolic formation, breakdown, and interconversion of carbohydrates.
• Carbohydrates are central to many essential metabolic pathways.
• Plants synthesize carbohydrates allowing them to store energy absorbed from sunlight internally. By photosynthesis.
• Cellular respiration breaks down these stored carbohydrates to make energy available to cells.
• Energy is stored in high energy molecules, such as ATP for use in various cellular processes.
• Digestion breaks down complex carbohydrates into simple monomers for metabolism which includes glucose, fructose, and galactose.
• Glucose constitutes about 80% of the products.
• The primary structure is distributed to cells in the tissues, where it is broken down or stored as glycogen.
• In aerobic respiration, glucose and oxygen are metabolized to release energy.
• Byproducts are carbon dioxide and water.
• Most of the fructose and galactose get converted to glucose in the liver.
• Simple carbohydrates have their own enzymatic oxidation pathways
• The disaccharide lactose is broken into its monosaccharide components, glucose and galactose

Metabolic Pathways

• Glycolysis
• Pentose Phosphate Pathway
• Glycolate Pathway
• Glycogenesis
• Gluconeogenesis
• Alcohlic Fermentation
• Citric Acid cycle

Glycolysis/Embden-Meyerhof Pathway

• Production of ATP with glucose oxidation to pyruvate and lactate.
• Quantitatively, it is the major pathway for glucose metabolism.
• Occurs in the cytoplasm of cells in the body.
• Required for energy generation, and the final product of glycolysis is either pyruvate or lactate.
• Pyruvate depends on the presence of oxygen or absence of it. Pyruvate eventually enters the Krebs cycle for further energy production.

Krebs Cycle/Citric Acid Cycle/Tricarboxylic Acid Cycle

• Acetyl-CoA is oxidized to carbon dioxide and water, with the release of ATP.
• The final oxidative pathway for all macronutrient metabolism in order to meet energy needs in most complex organisms.
• Lipids and carbohydrates are the main substrates in this cycle.
• Most importantly, this pathway provides building blocks for various processes. Includes processes such as synthesis of DNA, proteins, fatty acids, cholesterol, and steroids.
• Occurs inside the mitochondria of eukaryotic cells.

Gluconeogenesis/de Novo Glucose Synthesis

• Glucose synthesis from amino acids, glycerol, and other non-carbohydrate precursors.
• Is fundamentally a reversal of glycolysis pathway.
• The primary substrates are lactate, pyruvate, glycerol, and amino acids.

Ethanol Fermentation

• One glucose molecule breaks down into two pyruvates. This exothermic reaction has energy bind the inorganic phosphates to ADP and convert NAD+ to NADH.
• The two pyruvates are broken down into two acetaldehydes and give off two CO2 as a by-product.
• The two acetaldehydes convert to two ethanol.

Glucose as Fuel

• Glucose is a chemical fuel used to obtain energy, reducing power, and carbon skeletons.
• Glucose is the major form in which carbohydrates absorbed through the intestinal epithelium are presented to cells.
• Common dietary disaccharides are sucrose, maltose, and lactose.
• The intestinal epithelium splits disaccharides into monosaccharides then transports them to the blood.

Glucose Transport

• Different tissues take up glucose from blood depending on their glucose transporters (GLUTs).
• Blood glucose is maintained at about 5mM.
• Glucose transporters (GLUT) are integral membrane proteins that have 12 membrane-spanning domains.
• GLUT1 and GLUT3 are present on many cells, Km = 1 mM. Since blood glucose is usually maintained at about 5mM, GLUT1 and GLUT3 transport glucose at a constant rate independent of blood glucose concentration.
• GLUT 2 is present on liver and pancreatic beta cells, Km = 15 - 20 mM the rate of entry of glucose into liver and pancreatic beta cellsis proportional to the blood glucose levels.
• GLUT4 is present on muscle and fat cells, Km = 5 mM. Insulin controls entry of glucose, increases the number of GLUT4 molecules in the membranes of muscle and fat cells thereby controlling entry of glucose in these cells.
• GLUT5 is actually a fructose transporter.
• Brain and muscle use glucose as a major fuel.
• Brain also uses ketone bodies as fuel during severe starvation.
• Liver does not use glucose as its major fuel.

Energy Forms

• Chemical energy is converted through glycolysis, TCA cycle, and the pentose phosphate shunt of glucose into two forms:
  • high-energy phosphate bond of ATP.
  • electron donors NADH, FADH2 and NADPH

Glycolysis characteristics

• Glycolysis occurs in all cells.
• C6 -> 2 C3.
• Aerobic glycolysis produces a net gain of 2 ATP and 2 (NADH + H+).

Glycolysis - additional products

• Anaerobic glycolysis produces a net gain of 2 ATP
• NADH reduces pyruvate to lactate to regenerate NAD

TCA Cycle

• Loss of CO2 and gain of NADH occur in the conversion of pyruvate to acetyl CoA
• Only to a limited extent in fat cells and doesn't operate in red blood cells
• Limiting in exercising muscle in which the TCA cycle and oxidative phosphorylation can't keep up with the rate at which pyruvate is produced by glycolysis
• 2 CO2 is released during the final oxidation steps of entering acetatederived from acetyl CoA
• 1 ATP that is gained is the form of GTP 4 reducing equivalents are gained as 3 NADH and 1 FADH2
• Indirectly yields energy from NADH and FADH2 supplied to mitochondrial electron transport chain

Pentose Phosphate Shunt

• Happens in all cells, to different extents
• The oxidative branch yields 2 reducing equivalents, as 2 NADPH
• Gives 1 molecule of pentose (C5) phosphate from each glucose-6-phosphate
• NADPH is important for reductive biosynthesis. Red blood cells use NADPH to maintain a reduced environment.
• The non-oxidative branch interconverts phosphate sugars C5 C3, C4, C6, C7
• Glucose is stored as glycogen

Glycogen Storage

• In muscle, heart, liver BUT NOT- in brain, NOT in red blood cells
• Intracellular generation of glucose
• requires net utilization of energy

Glycogenesis

• Glycogen breakdown to glucose-1-phosphate and then convert glucose-6-phosphate

Glucose regulation

• Coordination of glucose breakdown is achieved by hormonal regulation

Glucagon, Insulin

• Pancreatic alpha cells secrete glucagon and causes the liver to release glucose to the blood.
• Pancreatic beta cells secrete insulin in response to glucose levels.
• Insulin promotes uptake of glucose by cells and storage in the liver.

Pathway of Glycolysis

• The major intracellular form of glucose is glucose-6-phosphate
• Phosphorylation of glucose to form glucose-6-phosphate by hexokinase
• Irreversible, regulated step; ATP is expended
• Feedback inhibited

Glucose characteristics

• The liver has a glucose buffer that assures constant glucose concentration
• Glucokinase biosynthesis is induced by insulin and has a high Km and high Vmax for glucose, and is not product-inhibited.
• Liver does not use glucose as preferred fuel. Conserves it for other tissues that require a primary fuel.
• Glucokinase gene transcription is repressed by glucagon

Glycolysis

1. Major intracellular form of glucose is glucose-6-phosphate
2. Glycolysis yields high energy phosphate

Regulation

1. Isomerization of glucose-6-phosphate (aldose) to fructose - 6- phosphate by phosphoglucose isomerase
2. Phosphorylation of fructose - 6 - phosphate to form fructose- 1, 6 - bisphosphate by phosphofructokinase- 1

• Rate limiting step and the most important site of regulation
• Allosteric inhibition
• Allosteric activation by fructose - 2 , 6 - bisphosphate

Glycolysis continued

3A. Phosphorylation of fructose-6-phosphate to fructose-2,6-bisphosphate 4. Cleavage of fructose - 1, 6 bisphosphate 5. Interconversion of dihydroxyacetone phosphate 6. Oxidation of glyceraldehyde - 3 - phosphate 7. Transfer of the high energy phosphate 8. Interconversion of 3-phosphoglycerate 9. Dehydration of 2-phosphoglycerate to from phosphoenolpyruvat 10. Transfer of high- energy phosphate bond 11. Regeneration of NAD +

Protein Basics

• Proteins are very large molecules composed of amino acids.
• They contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.
• These complex molecules are key to life, involved in metabolism, movement, defense, cellular communication, and molecular recognition.

Protein Functions

• Structural: Provide structure and strength (e.g., collagen, elastin, keratin).
• Dynamic: Act as enzymes, hormones, clotting factors, antibodies, receptors, and storage molecules, and function in genetic control, muscle contraction, and respiration.

Protein Composition

• Primarily carbon, hydrogen, oxygen, and nitrogen.
• Some proteins also contain other elements, such as P, Fe, Cu, I, Mg, Mn, and Zn.
• The nitrogen content of proteins averages 16%.
• Proteins are polymers of L-D-amino acids, which are obtained upon complete hydrolysis.
• Amino acids may be hydrophobic or hydrophilic.

Protein Structures

• Primary Structure: the sequence of amino acids
• Secondary structure: folding and twisting of acids to form beta sheets
• Tertiary structure: a folded three-dimensional figure
• Quaternary structure: Combining more than one protein to create a structure

Amino Acids

• Are organic compounds containing an amino and a carboxyl group.

Structural Properties of Amino Acids

• If both carboxyl and amino groups are attached to the same carbon atom.
• D-carbon atom binds to a side-chain which is different for each of the 20 a acids.
• Mostly exists in the ionized form in biological systems.

Optical Isomers of Amino Acids

• Exhibits optical isomerism.

4 Classes of Amino Acids

• Non polar
• Aromatic
• Basic
• Imino

Essential Amino Acids

• are acids cannot be synthesized by the body therefore they should come from the diet

Physical

• Solubility: soluble in water yet insoluble in organic solvents
• Melting points: melt at high temps
• Optical properties: all possess optical isomers
• Ampholytes: Contain both acidic and basic and can donate a proton..

Chemical Properties of Amino Acids

• Presence of the two functional groups mainly

Reactions

• salt formations with bases
• Undergo to decarboxylation.
• React with ammonia

Peptide Bond Formation

• Connects bond by alpha carboxyl groups with alpha acid.
• Proteins are made by the formation of polymers through synthesis

Color Reaction of Amino Acids

• Gives positive of amino is present of peptides
• Need high protein

Proteins Characteristics

• Are used to build the body through building an building to structural They are also known for coding abnormalities.

• Have primary oxygen, nitrogen and hydrogen, or carbon. The nitrogen average composition is 16 percent . Therefore it would be polymers Properties such that it is the chain

• Has a slight double bonded and is 'trans'

Tripeptides

Three amino acid in total and different acids and have combinations.

• Contains Glutamine which reduces or oxidants.. In summary proteins are composed of the important functions and that they build the body.