Introduction to Biochemistry

• Biochemistry combines biology, the study of life, and chemistry, the study of matter's composition, structure, and properties.
• Matter possesses volume and mass, encompassing both animate and inanimate objects.
• Organic chemistry focuses on carbon-containing compounds, crucial to all living things.
• Biochemistry studies chemical structures, compositions, and processes in living organisms, vital for understanding physiological processes.

Scope of Biochemistry

• The primary focus is the composition of living things, highlighting organic compounds.
• Organic compounds assemble into macromolecules or biomolecules: carbohydrates, lipids, proteins, and nucleic acids.
• Reactions among biomolecules create organelles, which form cells, leading to tissues and organs with specific functions.
• The source, digestion, and nutrition of biomolecules, along with metabolism catalyzed by enzymes, are key subjects.
• Chemical reactions within organisms, controlled by hormones, and the processing of end and waste products are studied.

Organization of Living Things

• Elements (C, H, O, N, P, S) form Biomolecules (carbohydrates, lipids, proteins, nucleic acids), which build Organelles (nucleus, cell membrane, etc.).
• Organelles combine to create Tissues, which form Organs, leading to Systems, and finally, the complete Organism.

Organic Compounds

• Organic compounds contain carbon, excluding cyanides, carbonates, bicarbonates, and oxides.
• Organic (soluble in non-polar solvents, combustible, easily decomposed, slow chemical reactions, covalent bonds) vs. Inorganic Compounds (soluble in polar solvents, non-combustible, not easily decomposed, fast chemical reactions, ionic bonds)

Bonding and Isomers

• Key elements in organic compounds include carbon (four bonds), hydrogen (one bond), oxygen (two bonds), and nitrogen, phosphorus, and sulfur (variable bonds).
• The variety of organic compounds arises from bond hybridization and isomer formation.

Hybridization of Carbon Bonds

• Sp3: Carbon reacts with four elements, resulting in four sigma bonds and single bonds.
• Sp2: Reaction with three elements forms three sigma bonds and one pi bond.
• Sp: Reaction with two elements forms two sigma bonds and two pi bonds.

Isomers

• Isomers have the same molecular formula but differ in structural formulas
• Example: Acetones and acetaldehydes, both with the formula C3H6O, have distinct structural arrangements.

Naming Organic Compounds

• Naming is based on the number of carbon atoms, using either IUPAC or common name prefixes.

• IUPAC Prefixes for Carbon Number:

• 1: Meth

• 2: Eth

• 3: Prop

• 4: But

• 5: Pent

• 6: Hex

• 7: Hept

• 8: Oct

• 9: Non

• 10: Dec Common Name Prefixes for Carbon Number:

• 1: Form

• 2: Acet

• 3: Propion

• 4: Butyr

• 5: Valer

• 6: Capro

• 7: Enanth

• 8: Capryl

• 9: Pelargon

• 10: Capr

• Suffixes depend on the compound's classification as hydrocarbon or hydrocarbon derivative.

• Hydrocarbons contain only hydrogen and carbon, classified as aliphatic (open chain) or alicyclic (closed chain).

• Aliphatic hydrocarbons are either saturated (single bonds, such as alkanes) or unsaturated (multiple bonds, such as alkenes and alkynes).

• Aromatic hydrocarbons contain a benzene ring (C6H6).

Organic Compound Classes and Formulas

• Alkanes: CnH2n+2
• Alkenes: CnH2n
• Alkynes: CnH2n-2
• Alcohols: ROH
• Amines: RNH2
• Ethers: ROR
• Carboxylic Acids: RCOOH
• Aldehydes: RCHO
• Ketones: RCOR
• Amides: RCONH2
• Esters: RCOOR
• Alcohols, aldehydes, and ketones are common in carbohydrates.
• Lipids are esters formed by reactions between carboxylic acids and alcohols.
• Amines and other organic compounds are present in amino acids; nucleic acids include amines, aldehydes, alcohol, and aromatic hydrocarbons.

Chemical Reactions in Living Organisms

• Reactions occur in the functional groups (active sites) of organic compounds.
• Hydrolysis: Water addition splits molecules, often catalyzed by enzymes or heat.
• Dehydration: Water removal joins molecules, occurring between two hydroxyl groups.
• Polymerization: Similar compounds unite to form a polymer.
• Addition polymerization: Molecules link together, incorporating double or triple chemical bonds in unsaturated monomers.
• Oxidation: Decrease in oxidation state, achieved by adding oxygen or removing hydrogen.
• Reduction: Increase in oxidation state, achieved by adding hydrogen or removing oxygen.
• Other reactions: Decarboxylation removes the carboxyl group; transamination transfers the amine group; phosphorylation adds a phosphate group.

The Cell and Its Organelles

• All living organisms consist of cells, the basic functional unit capable of growth, metabolism, reproduction, irritability, and adaptation.
• Cells are classified as prokaryotic (no nuclear membrane; simple chromosome near the cell membrane; free ribosomes; e.g., bacteria) or eukaryotic (nuclear membrane; membrane-bound organelles; e.g., plant and animal cells).

Plant vs. Animal Cells:

Plant Cells:

• Large central vacuole
• Plastids
• Cell wall Animal Cells:
• Small food vacuole
• No plastids
• No cell wall

Cell Organelles

• Cell Membrane:
• A delimiting membrane that regulates substance passage, recognizes substances, protects from harm.
• Composed of a fluid phospholipid bilayer with embedded cholesterol for rigidity and mosaic proteins (channel and carrier).
• The Glycogen can combine with proteins (glycoprotein) or lipids (glycolipids).
• Biomolecules present include carbohydrates, proteins, and lipids.
• Nucleus:
• Serves as the command center due to chromosomes containing DNA for RNA synthesis and protein production.
• Contains a nucleolus for active RNA synthesis.
• Protected by pore-filled nuclear membrane, with similar composition to the cell membrane.
• Biomolecules present: carbohydrates, proteins, lipids, nucleic acids (DNA and RNA).
• Endoplasmic Reticulum (ER):
• Extension of the nuclear membrane, classified as smooth ER (no ribosomes; synthesizes carbohydrates and lipids) or rough ER (ribosomes; synthesizes proteins).
• Smooth ER: carbohydrates, lipids, and proteins.
• Rough ER: carbohydrated, lipids, proteins, and RNA
• Golgi Bodies:
• Flat vesicles package carbohydrates, lipids, and proteins from the ER.
• Can combine molecules to form glycoproteins and lipoproteins.
• Proteins/enzymes can develop into lysosomes.
• Biomolecules present: carbohydrates, lipids, and proteins.
• Lysosomes:
• Contain hydrolytic enzymes for splitting molecules via water addition.
• Capable of digesting substances and non-functional organelles (scavengers).
• Can cause self-destruction (autolysis) by releasing enzymes into the cytoplasm.
• Biomolecules present: carbohydrates, lipids, and proteins.
• Mitochondria:
• Has A structure similar to prokaryotic cell with inner/outer membranes.
• Inner membrane foldings (cristae) increase surface area for oxidative phosphorylation, producing ATP.
• It is the Power house of the cell
• Can self-regulate and self-replicate, containing a simple chromosome.
• Biomolecules present: proteins, lipids, carbohydrates, DNA, and RNA.
• Non-Membrane Bounded Organelles:
• Microfilaments: Composed of actin and myosin for cytoplasmic movement and organelle support.
• Centrioles: Made of tubulin, forming asters and spindle fibers for chromosome movement during cell division.

Inorganic Components of the Cell

• Water: A universal polar solvent facilitating chemical reactions; maintains osmotic pressure and temperature regulation.
• Ions: Positively charged cations or negatively charged anions essential for nerve impulse conduction, contributing to cell irritability.
• Salts: Act as inorganic buffers to maintain neutral pH, prevent protein denaturation, and enzyme destruction, in and out of of the cell.
• Gases: Oxygen (used in oxidation reactions and ATP formation) and carbon dioxide (waste product, converted into carbohydrates during photosynthesis in plants).

Carbohydrates

• Organic compounds of carbon, hydrogen, and oxygen with the formula Cx(H2O)y that include proteins, lipids and nucleic acids.

• They Functions range from energy storage/transport to structural components, broken down during metabolism.

• Formula: C6H12O6 + 6 O2→6 CO2 + 6 H2O + energy

• In reverse: 6 CO2 + 6 H2O + energy (from sunlight)

• Carbs Structural components:

• cell surfaces, ATP(energy component)

• DNA,

• RNA,

• the immune system,

• Are called saccharides or sugars,

• Three Classes: Monosaccharides, Disaccharides, Polysaccharides

Classification of Carbohydrates

• Are called saccharides or sugars, classified according to the number of saccharide molecules.
• Monosaccharide
• Disaccharides
• Polysaccharides

Monosaccharide

• Monosaccharides: Simplest carbohydrates that cannot be hydrolyzed.
• Classified by: carbonyl group location (aldose if aldehyde, ketose if ketone), carbon number, and chiral handedness.
• List includes glucose (dextrose), fructose, galactose, xylose, and ribose
• They function as building blocks of disaccharides (sucrose) and polysaccharides (cellulose, starch).

Common Monosaccharides:

• Trioses:

• Aldotriose: glyceraldehyde

• Ketotriose: dihydroxyacetone · Tetroses:

• Aldotetrose: erythrose and threose

• Ketotetrose: erythrulose · Pentoses:

• Aldopentoses: arabinose, lyxose, ribose, deoxyribose, and xylose Ketopentoses: ribulose and xylulose · Hexoses:

• Aldohexoses: allose, altrose, galactose, glucose, gulose, idose, mannose and talose

• Ketohexoses: fructose, psicose, sorbose and tagatose · Heptoses:

• Keto-heptoses: mannoheptulose, sedoheptulose

• Octoses: octolose, 2-keto-3-deoxy-manno-octonate

• Nonoses: sialose

• Trioses: Monosaccharides with 3 carbons that are important in respirations.

• Aldotriose (glyceraldehyde

• Ketotriose (dihydroxyacetone)

• Tetroses:

• monosaccharide with carbon 4

• an aldehyde functional group in position 1 (aldotetroses) or a ketone functional group in position 2 (ketotetroses).

• aldotetroses have two chiralatrial centres and 4 stereoisomers: erythrose, threose, D-Erythrose, D-Threose D-Erythrulose

• Pentoses:

  • Monosaccharide consist of five carbon atoms, which are:
  • Aldopentoses- Aldehyde functional group in position 1 which are: D-Ribose, D-Arabinose, D-Xylose, D-Lyxose
  • Ketopentoses- Ketone functional group in position 2

Cyclic structure

• hemiacetals or hemiketals (depending on whether they are aldoses or ketoses) between an alcohol and the carbonyl group of the same sugar.
• Glucose, readily forms a hemiacetal linkage between its carbon-1, hydroxyl group on its carbon-5.
• Two anomers are formed (a-isomer vs. β-isomer) that interconvert due to mutarotation.
• a-isomer has the OH- of the anomeric carbon under the ring structure.
• β-isomer, has the OH- of the anomeric carbon on top of the ring structure.
• Only natural hexoses are capable of of being fermented by yeasts

Isomerisms

• Stereoisomers: Molecules with identical constitution, differing in spatial arrangement.
• Enantiomers: Mirror images, non-superimposable, same properties except for polarized light rotation.
• Optical activity needs chiral agents for separation.
• Diastereomers: Are not mirror images,include meso compounds and cis-trans isomers
• Trans and E-Z double bounds stereoisomerism: Substituents same.

Conformers

• Conformational isomerism describes molecules same formula but different shapes by a rotation, molecules rarely isolatable.
• Monosaccharides: Major source of energy, or converted into polysaccharides animals this is glycerol, expecially in liver and muscle cells.

Disaccharides

• Is where two monosaccharides join with glycosidic linkage via dehydration.
• Formula: C12H22O11.
• The systematic name O-a-D-glucopyranosyl-(1→2)-D-fructofuranoside shows monosaccharides, ring types, linkage, and anomeric carbon involvement.

The Common Disaccharides:

• Sucrose: Most abundant, composed of glucose and fructose, transporting energy in plants
• Lactose: Composed of galactose and glucose with enzyme lactase mostly in animals
• Mammals infant: fed on milk with its enzyme lactase/β-D-galactosidase secreted the intestinal villi where they are absorb glucose for digestion.

Ethnic lactose

• Europe, Middle East, India, east Africa maintain lactase into adulthood.

Different glycosidic bonds

• Alpha or beta combinations result different with bond combinations, (regiochemistry) and stereochemistry chemical properties.

Lactose Intolerance

• the inability to absorption lactose in blood stream so is uncleaved and passes to the colon.
• operons of bacteria result from:
• produces hydrogen, carbon dioxide, methane.
• abdominal causes range stomach cramps, bloating, and flatulence
• prevents water absorption

Types of intolerance

• Primary intolerance environmentally induced of no commercial diary
• Secondary where gastroenteritis rotavirus and disrupt lactase production .
• genetic disorder prevents lactase

Other Disaccharides

• Maltose: Composed of two glucose, produces maltose by amylases, Enzyme is catalyst breaking glucose for germination in cereals, such as barley is sugars.
• Ethanol +carbon dioxide produces Metabolism

The Common disaccharides

• Sucrose
• Lactose
• Maltose
• Trehalose
• Cellobiose
• Maltose and cellobiose are hydrolysis products of the polysaccharides, starch and cellulose, respectively.

OLIGOSACCHARIDES

• A saccharide polymer containing a small number of component sugars. Fructo-oligosaccharides (FOS) consist of short chains of fructose molecules and Inulin has a much higher degree of polymerization than FOS. Galactooligosaccharides (GOS) consist of short chains of galactose molecules. Oligosaccharides are often found as a component of glycoproteins or glycolipids such as used as chemical markers .

POLYSACCHARIDES

• Large molecules joining monosaccharide by glycosidic bonds (glycans).
• Cellulose, starch and glycogen consist of alpha-glycoside links or beta-glycoside links
• Cellulose is a glucose and its fibres are used by plants for food, also the beta-glycoside bonds are stabilized intramolecular and intermolecular hydrogen bonds.
• Starch is used for roots, rhizomes, seed depend nourishment , its structure is granules are burst,
• Amylose which units joined glycoside chains that can causes bursts: or is Much molecules and dispersion.
• Amylopectin higher than amylose but are water insoluble because consists links is

Lipids and Related compounds

• Heterogenous compounds related of fatty acids by tissues by polar solvents, a fuel to protective coats.

Classfy

• Simple fatty acids ester by alcohols a liquid fat is oils or higher molecular called waxes
• complex are other group by ester include phosphatidic alcohol a fatty ester also glycolic acid(sphingolipids) the sphingo the fatty acid.
• Precursor the products showing physical characteristics .
• glyceroids, sterols.

LIPIDS SOURCES

• plant reserves for energy.
• Fatty depots inside body
• compound of sterols
• Fatty Acids abundant ester the building Blocks, has hydrocarbon of carboxyl, can chain of carbon even if
• Saturated fatty acids +ic or IUPAC single low
• Unsterols reactive the EIC reactive.

The fats and triglycerids

• R = glycerol by palimate as in castor more alkali called ester as for
• Wax neutral chains called beewax
• complex ester the alcohols and phosphoric

phosphoglycerides

• sometimes called phospholipids esters alpha +alphatic a more saturated palmitic as lecithin esteriolamines particularly substance as licositol. the glycolids by chains of ceramide.

Sphingolipids

• sphingomyelins + brain
• cerebrocosmic the matter. Gangilosides cell.

Prostaglandins

• of 14 chainic reaction influx

Steroids

• separate cycilc in animal but

Ergostenol-

under skin D bacterias bile Sterole

FUNCTIONS

• membranes store
• transfers by insects
• membrane specificity

PROTEINS

• cells which functions

Composition

• asymmetrical.

Amino acids

• acid glutamic, acid, arginine
• Chain alanine is leucine isoline, chain phenylanie
• Amino acids acids

Peptide formation

Elimination chain

levels

amino with protein

Properties

temperature to certain

Chemical chain to cells

and shapes acid

FUNCTIONS

• reactions tissue molecules hormones

Biochemistry combines biology and chemistry, focusing on the composition, structure, and properties of matter. It studies chemical structures, compositions, and processes in living organisms, vital for understanding physiological processes. The primary focus is the composition of living things, highlighting organic compounds and their reactions.