Biochemistry: Elements, Isotopes, and Radioisotopes

• Biochemistry is the study of the chemistry of molecules that constitute life and their interactions within living organisms, focusing on the physical and chemical properties of biological compounds.
• Matter is anything that occupies space and possesses mass.
• Life is composed of 92 naturally occurring elements, with 25 being essential.
• Carbon and hydrogen serve as the fundamental building blocks of biological molecules.
• Nitrogen, phosphorus, sulfur, and oxygen work together with carbon and hydrogen to provide chemical properties.

Isotopes

• Isotopes are variants of an element with the same number of protons but differing neutron counts.
• Protons define an element, and most have one or more stable isotopes.

Radioisotopes

• Radioisotopes are unstable isotopes due to an imbalance in neutron count.
• They undergo spontaneous nucleus decay by emitting subatomic particles or electromagnetic waves.

Radioactive Decay

• Radioactive decay occurs to stabilize the nucleus and converts one element to another; the more unstable the radioisotope, the faster the decay.

Uses of Radioisotopes

• Radiotherapy employs radioisotopes to destroy cancer cells.
• Radioisotope tracing uses detectable radioactive substances to follow biological processes.
• Radiometric dating infers the age of rocks and fossils by measuring the ratios of isotopes and their decay products.

Half-Life

• Half-life is the period it takes for half of a radioactive sample to decay.

Intramolecular Forces

• Intramolecular forces hold atoms together within a molecule.

Ionic Bonds

• Ionic bonds are the electrostatic forces between oppositely charged ions and easily broken in polar solvents.

Covalent Bonds

• Covalent bonds involve sharing electrons to achieve a full valence shell.

Electronegativity

• Electronegativity describes an atom's ability to attract shared electrons.
• Elements vary in electronegativity.

High Electronegativity

• Oxygen, Nitrogen, and Chlorine exhibit high electronegativity.

Low Electronegativity

• Hydrogen, Carbon, and Phosphorus exhibit low electronegativity.

Polar Covalent Bonds

• Polar covalent bonds form from unequal electron sharing between elements with differing electronegativity.
• They create partial positive and negative charges within the molecule.

Nonpolar Covalent Bonds

• Nonpolar covalent bonds occur between elements with similar electronegativity values.

Intermolecular Forces

• Intermolecular forces are attractive forces between molecules affecting substance physical properties.
• Examples include hydrogen bonding and hydrophobic interactions.

Hydrogen Bonding

• Hydrogen bonds occur between hydrogen atoms bonded to electronegative atoms like oxygen, nitrogen, or fluorine.
• These are weaker than covalent or ionic bonds, but collectively strong.

Hydrophobic Interactions

• Hydrophobic interactions occur between nonpolar molecules and water, resulting in clumping due to the exclusion from water.

Hydrophilic Interactions

• Hydrophilic interactions occur between polar molecules and water, facilitating hydrogen bond formation.

Hydrophobic Effect

• The hydrophobic effect is the phenomenon where non-polar molecules aggregate in the presence of water.

Functional Groups

• Functional groups are specific atom groups attached to molecules that dictate chemical and physical properties.

Hydroxyl Properties

• Hydroxyl groups are not highly reactive but readily form hydrogen bonds, increasing a molecule's water solubility.
• They are in carbohydrates, proteins, nucleic acids, alcohols and lipids.

Carbonyl Properties

• Carbonyl groups increases the water solubility of a molecule.
• They are found in carbohydrates and nucleic acids.

Carboxyl Properties

• Carboxyl groups are acidic and can donate a proton, acting as weak acids.
• They ionize by releasing a hydrogen ion from the hydroxyl group, leaving a negative charge with carboxyl group.
• They are present in proteins and lipids.

Amino Properties

• Amino groups are basic and accept protons, exhibiting some water solubility that decreases with increasing carbon count.
• Amino groups ionize by accepting a hydrogen ion, becoming positively charged.
• They are in proteins and nucleic acids

Sulfhydryl Properties

• Sulfhydryl groups are less polar than hydroxyl groups and have a strong odor, with lower boiling points and water solubility than comparable alcohols.
• Two sulfhydryl groups can react to form disulfide bonds

Phosphate Properties

• Phosphate groups are involved in energy storage and release through bond breakage, as well as linking nucleotides in nucleic acids.
• Found in nucleic acids, ATP, DNA, and RNA.

Molecular Formula

• Molecular formula indicates the types and numbers of elements in a molecule.

Structural Formula

• Structural formula indicates the atomic bonding arrangement within a molecule.

Isomers

• Isomers have identical sets of atoms but differ in arrangement, leading to distinct properties.

Structural Isomers

• Structural isomers exhibit variations in their bonding arrangements.

Stereoisomers

• Stereoisomers exhibit variations in the spatial orientation of their groups.

Positional Isomerism

• Positional isomerism features the same functional group at different locations in the molecule.

Chain Isomerism

• Chain isomerism has differing carbon backbones.

Functional Isomerism

• Functional isomerism has different functional groups present.

Geometric Isomerism

• Geometric isomerism has similar bonding patterns but different arrangements around a double bond.
• Cis isomers have like groups on the same side; trans isomers have like groups on opposite sides.

Enantiomers

• Enantiomers share molecular formula and connectivity, but aren't superimposable, behaving as mirror images.
• They occur with asymmetrical carbons, bound to four unique groups.

Carbohydrates

• Contain C, H, and O in the ratio of CnH2nOn .
• They are generally polar and water-soluble due to numerous hydroxyl and carbonyl groups.
• Carbohydrates serve as sources of short term energy or long term energy storage.

Carbohydrates - Monosaccharides

• Monosaccharides contain 3-7 carbon atoms, numerous OH groups, and are water-soluble.
• Examples include glucose, fructose, and galactose.

Glucose Stereoisomers

• The position of the OH group on carbon 1 determines if glucose is alpha or beta.
• Both forms exist when dissolved in water. alpha has the OH on the bottom, and beta has the OH on top.

Disaccharides

• Formed when two monosaccharides are linked via a glycosidic bond.
• 1-4 linkages form chains, and 1-6 linkages create branches.

Sugar Equations

• Glucose + fructose yields sucrose.
• Glucose + glucose yields maltose.
• Glucose + galactose yields lactose.

Amylose and Amylopectin

• Amylose is unbranched, making up 20% of starch.
• Amylopectin is branched, accounting for 80% of starch.

Starch vs Glycogen

• Both are energy storage units, but glycogen's highly branched structure facilitates faster breakdown for energy due to its greater surface area.

Cellulose

• Cellulose is a major component of plant cell walls, featuring beta-glycosidic bonds that humans cannot digest due to a lack of the necessary enzyme.
• It high in fibre but has no nutrient value.

Alpha vs Beta Glycosidic Linkage

• Alpha linkages have joining monomers with OH groups in the same orientation.
• Beta linkages have joining monomers with OH groups in opposite orientations.

Lipids

• Lipids contain C, H, and O, with higher proportions of C and H and lower proportions of O.
• They are hydrophobic but soluble in oils and nonpolar solvents, serving as major energy storage molecules.
• Yields twice more energy than carbohydrates
• Examples include oils, fats, waxes, phospholipids, and steroids.

Functions of Lipids

• Lipids for long-term energy storage and insulation.
• Steroid hormones, protection, and serve as major components of cell membrane.
• They are responsible for the water-repellent layer on fruits, leaves, fur, and feathers.

Triglycerides

• Triglycerides consist of one glycerol molecule and three fatty acids linked by ester bonds.
• Glycerol is a three-carbon molecule with an OH group attached to each carbon.
• Fatty acids consist of a long hydrocarbon chain with a carboxyl group at one end.

Types of Fatty Acids

• Saturated fatty acids have only single bonds.
• Monounsaturated fatty acids contain at least one double bond.
• Polyunsaturated fatty acids contain two or more double bonds.
• Trans fatty acids contain a trans double bond.

Hydrogenation

• Hydrogenation adds hydrogen to liquid oil, converting it to solid fat.
• This process converts cis fats to trans fats.

Phospholipids

• Phospholipids differ from triglycerides by having two fatty acids instead of three, with the third position occupied by a phosphate and choline group.

Phospholipid Bilayer

• Phospholipid bilayer serves as the main component of cell membranes with hydrophilic heads facing aqueous environments and hydrophobic tails forming the interior.

Steroids

• Steroids are lipids with four fused carbon rings.
• The arrangement of rings and functional groups determines the steroid type.
• Examples include cholesterol, testosterone, estrogen, steroid ointments, and anabolic steroids.

Waxes

• Waxes are solid at room temperature and produced by plants and animals.
• In plants, waxes help prevent water loss and repel insects.
• In animals, provide a water-repellent layer on skin, fur, feathers, and exoskeletons.

Proteins

• Proteins have one or more polypeptides folded into globular or fibrous forms, with 20 types of amino acids.
• Amino acids are monomers with a central carbon attached to an amino group, carboxyl group, and a side chain.

Amino Acids

• Eight of the twenty amino acids are essential and must be obtained from food.
• Proteins vary in amino acid sequence and number.
• Polypeptides are chains of amino acids linked by peptide bonds.
• The number of possible protein sequences is 20^n, where n is the number of amino acids.

Functions of Proteins

• Proteins function as structural fibres and support, enzymes, aid in muscle movements, transport ions across the cell membrane, provide antibodies, and regulate cellular processes.

Types of Protein Structures

• Primary structure is the linear amino acid sequence.
• Secondary structure includes alpha helices and beta-pleated sheets formed by hydrogen bonds between amino and carbonyl groups.
• Tertiary structure involves complex folding with hydrogen bonds, ionic bonds, hydrophobic effect, and disulfide bridges.
• Quaternary structure comprises multiple polypeptides folded, with chains having their own 1, 2, and 3 structures.

Denaturation

• Denaturation occurs when intermolecular bonds break due to environmental changes, causing the protein to lose its three-dimensional structure and function.
• Causes include changes in pH, temperature, salinity, chemical environment, and agitation.

Nucleic Acids

• Nucleic acids store genetic information, with subunits of nucleotides.
• Nucleotides contain a five-carbon sugar, phosphate group, and nitrogenous base.
• Nitrogenous bases: adenine, guanine, cytosine, thymine, uracil

Type of Nucleic Acids

• RNA (ribonucleic acid) is a single nucleotide chain with ribose sugar and uracil instead of thymine.
• RNA carries information from DNA to ribosomes for protein synthesis and forms ribosomal structures.
• DNA (deoxyribonucleic acid) is a double helix with deoxyribose sugar.
• Contained in the nucleus and contains genetic information, with specific nucleotide sequences forming genes.

Bonds in DNA and RNA

• Complementary base pairs: A=T (or A=U in RNA) and G≡C.
• Phosphodiester bonds link the phosphate group of one nucleotide to the OH of the sugar of another.

Cell Membrane

• Cell membrane is semi-permeable and regulates the movement of ions and molecules in and out of the cell.

Fluid Mosaic Model

• The phospholipid bilayer is fluid, held together by intermolecular forces with continual rearrangement of lipids, allowing flexibility and self-healing.
• Membrane is a mosaic composed of various proteins, lipids and carbs. Glycoproteins and glycolipids are on the membrane surface and play roles in adhesions recognition and communication

Fluidity of Cell Membranes

• Fluidity increases with higher temperature and more double bonds but decreases with longer fatty acid tails.
• Cholesterol has the opposite effect of temperature, decreasing fluidity at higher temperatures and increasing fluidity at lower temperatures.

Cell Membrane Proteins

• Peripheral proteins remain on the perimeter of the phospholipid bilayer.
• Integral proteins include transmembrane proteins, which span the entire membrane, and proteins that are integrated into the membrane.

Functions sof Membrane Proteins

• Transport substances, catalyze reactions, cell recognition, and signal reception and transduction.

Passive vs Active Transport

• Passive transport moves substances down the concentration gradient without energy. (simple diffusion, osmosis, facilitated diffusion)
• Active transport moves substances against the concentration gradient with energy. (primary active transport, secondary active transport)

Diffusion- Passive Transport

• Diffusion moves substances from high to low concentration areas without energy.
• Dynamic equilibrium is reached when concentrations inside and outside are equal.

Osmosis- Passive Transport

• Osmosis is the movement of water from high to low concentration.
• Regulation of osmosis is crucial for maintaining cellular processes.

Osmotic Concentration

• Osmotic concentration refers to the concentration of all solutes in a solution.
• Isotonic solutions have the same osmotic concentration.
• Hypertonic solutions have more solute.
• Hypotonic solutions have less solute.

Facilitated Diffusion- Passive Trasort

• Facilitated diffusion moves polar molecules and ions down the concentration gradient across the membrane using channel proteins or carrier proteins.

Channel Proteins

• Channel proteins are highly specific for ions and small polar molecules.
• Protein structure, with one or more helices, determines the type of molecule transported.
• Hydrophobic amino acids on the exterior interact with the lipid bilayer, while polar amino acids line the interior to allow polar molecules to pass through.
• Some channels are gated, others are open.

Carrier Proteins

• Carrier proteins bind to specific, usually large, molecules and change shape during transport.
• Transport rate is slower than channel proteins.
• Hydrophobic amino acids on the exterior interact with the lipid bilayer, while amino acids lining the interior form intermolecular forces with the transported molecule.

Primary Active Transport

• Primary active transport uses ATP to move ions or molecules against the concentration gradient via carrier proteins.

Na+/K+ Pump

Electrochemical Gradient

Secondary Active Transport

Membrane Assisted Transport

• Membrane assisted transport moves macromolecules too large for channel/carrier proteins via vesicle formation.
• Requires energy. Types include endocytosis and exocytosis.

Endocytosis

• Endocytosis engulfs material from extracellular fluid, forming vesicles for transport into the cell.
• Phagocytosis engulfs solid particles and some liquid.
• Pinocytosis engulfs liquid with solutes.
• Receptor-mediated endocytosis uses receptor proteins in coated pits to bind specific molecules, folding inward to form a vesicle; receptors may be recycled.

Exocytosis

• Exocytosis fuses vesicles with the cell membrane to release products and wastes into the extracellular fluid.
• Vesicles become part of the cell membrane.
• Used in plants for cell wall construction and in animals for secretion of hormones, neurotransmitters, and digestive enzymes.

Study of biochemistry, focusing on the chemistry of molecules that constitute life and their interactions within living organisms. Matter, life's composition of elements, and the role of carbon, hydrogen, nitrogen, phosphorus, sulfur, and oxygen are also explored. Isotopes and radioisotopes are introduced.