SBI4U Unit One - Biochemistry Notes (PDF)

SBI4U - Unit One - Biochemistry Bonding Ionic Bonds dissociate easily in water one or more electrons transferred between atoms with an electronegativity of greater than 1.7 results in cation and anion soluble Covalent Bonds share electrons between atoms three t...

SBI4U - Unit One - Biochemistry Bonding Ionic Bonds dissociate easily in water one or more electrons transferred between atoms with an electronegativity of greater than 1.7 results in cation and anion soluble Covalent Bonds share electrons between atoms three types: polar unequal sharing of e- pairs EN between 0.41 and 1.7 eg. H2O nonpolar equal sharing of e- electronegativity of less than 0.4 eg. H2, O2, N2, CO2, CH4 amphiphilic some larger molecules have parts that are polar and parts that are nonpolar eg. fatty acids Note - like dissolves like, so polar dissolves polar, nonpolar dissolves nonpolar Electronegativity determines the strength of the bond F (fluorine) has the highest EN (highest “pull” of e-) has to do with the distance between valence e- and nucleus even though e- are being shared, one element may have a stronger “pull” can lead to the formation of polar molecules  the shape of molecules is related to their polarity Intermolecular Forces (aka van der Waals Forces) Hydrogen bonds attractive force between a partially positively charged hydrogen atom and a partially negative charge in another molecule eg. forces between water molecules Other van der Waals Forces weak, momentary attractions of one molecule to the nuclei of another molecule eg. London dispersion forces, dipole-dipole forces Chemical Reactions Dehydration Reaction (aka Condensation) Removal of an OH and H to join smaller molecules and make H2O eg. occurs naturally in plants, including sugarcane and sugar beets, from which we refine the sugar into pure table sugar Hydrolysis Reaction Adding water as OH and H splitting a larger molecule eg. happens in digestion in your stomach under the influence of the enzyme lactase Neutralization Reaction Between acids and bases to form water and salt eg. digestion - pancreas releases sodium bicarbonate and it is added to the small intestine to increase pH Redox Reaction Electrons are lost from one atom and gained by another eg. Aerobic Cellular Respiration: burning of fuel/glucose to produce energy LEO - Lose Electrons Oxidation GER - Gains Electrons Reduction Water Polar Covalent Bonds  Oxygen has a higher EN than hydrogen Hydrogen Bonds Electrons spend more time near the O than the H Cohesion  Water molecules are attracted to other water molecules Adhesion Water molecules attach to other polar molecules Capillary Action Adhesion and Cohesion working together Climbs inside tubules up to 90m Surface Tension Water molecules bond with their neighbours beside and below them BUT there are more bonds at the surface Lower Density Solid Water expands when freezing and becomes less dense This is why ice floats Life persists when lakes freeze over because the ice stays on top Spring/Autumn Turnover  The turnover and shifting of water throughout a body of water Warm water stays on top, cold water sinks Oxygenates the deep water and releases sulfurous gases High Heat of Vaporization Intenseheat and exercise may generate 1L of sweat per hour and 600 calories burned per litre of sweat evaporated When sweat evaporates, it pulls the heat with it, cooling us down High Heat Capacity Large amounts of heat are required to raise the temperature of water This is one of many reasons why rising ocean temperatures are so dangerous and concerning Universal Solvent Ionic and Polar substances dissolve in water Properties Summary: (WILL BE ON THE TEST) Low density solid Universal solvent High heat capacity Heat of vaporization Adhesion/cohesion Capillarity Surface tension The Carbon Chemistry of Life Carbon Chains Carbon atoms are the backbone of biochemistry Carbon atoms form the basis of the most complex molecules due to their ability to make 4 bonds, allowing for single, double, and triple bonds (as well as combinations of these bonds) Functional Groups  Commonly found in large molecules React in predictable ways Include amino (NH2), carboxyl (COOH), carbonyl (CO), hydroxyl (OH), peptide (CHON), phosphate (PO4) Macromolecules Carbohydrates Lipids Nucleic Acids Proteins Carbohydrates CHO - made up of carbon, hydrogen, and oxygen Monosaccharide - Disaccharide - Polysaccharide Monosaccharides CHO 1:2:1 Soluble (polar alcohols - OH) eg. glucose (C6H12O6), fructose Energy is readily available and easily transported Disaccharides Condensation (aka dehydration) reaction occurs when two monosaccharides combine, creating a disaccharide and H2O Hydrolysis uses H2O to break disaccharides back down into monosaccharides Glycosidic bond  Transportable energy in plants and animals eg. sucrose, maltose, lactose Polysaccharides Enzymes that digest α linkages can’t hydrolyze β linkages The cellulose passes through the digestive tract as “insoluble fibre” Many herbivores, from cows to termites, have symbiotic relationships with microbes that have enzymes to digest cellulose Polysaccharides - structural β-linkages have alternating orientation of monosaccharides examples: cellulose: long fibrous strings for structural support in plant cell walls chitin, embedded in proteins, forms arthropod exoskeletons and is used to make strong and flexible surgial thread Polysaccharides - storage α gycosidic linkages have uniform orientation of monosaccharides glycogen - glucose eg. organelles called leukoplasts store energy in plant roots as starch (amylose, amylopectin) Summary - Carbohydrates Functions: energy transport and storage, structural support Structure: monosaccharides - polysaccharides eg. glucose, lactose, starch, glycose, cellulose Functional groups: hydroxyl, carbonyls (aldehydes and ketones) (CARBONYLS ONLY SOMETIMES) Gycosidic bonds Lipids CHO(P) No monomers and no polymerization Nonpolar (hydrophobic) Monoglycerides - Diglycerides - Triglycerides  Glycerol Fatty acid(s) Ester bond Essential unsaturated fatty acids are not synthesized in the human body and must be supplied in the diet eg. Omega-3 fatty acids Omega-3 fatty acids have one of their carbon-carbon double bonds at the 3rd carbon atom at the end of their carbon chain Fat Functions Store energy Insulate Cushioning Nerve impulse transmission Phospholipids Form cell membranes Amphiphilic polar head (hydrophilic) nonpolar tail (hydrophobic) Other Fats Messengers (hormones) blood pressure sexual characteristics growth Protection waxy layer on leaves and fruit prevents invaders from entering tissue, dehydration Summary - Lipids Functions - energy storage, membranes, messengers Structure - straight chains (fatty acids) and rings eg. testosterone, cholesterol, beeswax Functional groups - carboxyl, hydroxyl Ester bonds Nucleic Acids CHONP DNA - deoxyribonucleic acid RNA - ribonucleic acid Nucleodies - monomers Bonding Covalent bonds Phosphodiester bonds H- bonds Proteins CHON(S) Amino acids (monomers) - dipeptide - polypeptide Amino Acids R group 1-20 eg. glycine, alanine Polar, nonpolar, electrically charged Dipeptides Polymerization (anabolic) Condensation (catabolic) Breaking apart (hydrolysis) Protein Functions  Enzymes - catalyze reactions eg. lactase Antibodies - fight invaders eg. viruses Hormones - chemical messengers eg. insulin Hemoglobin - transports O2 in RBC Movement - actin, myosin, etc. muscles, cilia, flagella Support - collagen, elastin, keratin tendons, ligaments, hair, horns, nails, feathers, quills Nutrient Storage - albumin, amandin amino acids for developing plant/animal embryos Protein Organization Primary sequence of amino acids coded by DNA (peptide bonds) Secondary α helix and β sheet (H- between polar R’s) Tertiary 3D shape is globular or fibrous (various bonds) Quaternary 2 or more polypeptides join (becomes a functional protein) Proteins Denature Nonfunctional Bonding in the tertiary structure is disturbed Caused by: Temperature pH Salt concentration Summary - Proteins Functions - transport, movement, messengers Structure - 20 different amino acids - polypeptides eg. enzymes, hemoglobin, anitbodies, hormones Functional groups - amine, carboxyl Bonds - peptide EVERYTHING ABOVE THIS POINT IS ON THE UNIT ONE QUIZ Cell Membranes Types of Cells can be prokaryotic eg. bacteria cells can be eukaryotic eg. plant and animal cells Eukaryotic Cells organelles are the cell parts the amount of each type of organelle varies by cell type eg. muscle cells contain many mitochondria eg. white blood cells contain many lysosomes eg. pancreatic cells that make insulin contain a lot of rough ER The Cell Membrane Functions maintain cell shape allows some things to enter/exit (semi-/selectively permeable) commication with other cells show cell identity Fluid Mosaic Model flexible made of many different parts phospholipid bilayer with protein embedded throughout molecules are attracted to each other but float freely Phospholipids form a bilayer spontaneously hydrophilic heads associate with water inside and outside of the cell nonpolar tails form hydrophobic inner layer Carbohydrates (part 2!!!) markers that identify the cell glycoproteins “person specific” so the immune system can recognize “invaders” eg. sometimes transplants are rejected because of these markers glycolipids “tissue specific” so cells stop multiplying and stay put eg. metastasized tumors ignore these markers Cholesterol contributes to the fluidity of the membrane reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification Globular Proteins receptors for communication transport substances in and out speed up reactions anchors cells and their parts two types integral embedded in protein peripheral attached to surface Fibrous Proteins form a cytoskeleton to maintain cell shape shape is closely tied to function Passive Transport small particles diffuse across a membrane from high concentration to low concentration until an equilibrium is reached Osmosis the diffusion of water across a membrane Simple Diffusion movement of molecules from an area of [high] to [low] across a membrane small molecules (O2, CO2) nonpolar molecules only (steroids, amino acids) Facilitated Diffusion requires a specific protein channel moves down concentration gradient requires no energy large, polar molecules (glucose, fatty acids, amino acids) ions require channel proteins (K+, Cl-, Na+, H+) Solutions solvent - substance that dissolves the solute (eg. water) solute - substance that dissolves in the solvent Hypotonic lower concentration of solute than inside the cell in animal cells, this is dangerous - the cell may burst in plant cells, the cell membrane pushes against the cell wall Turgor pressure increases = turgid (firm, healthy) Hypertonic higher concentration of solute than inside the cell in animal cells, the cell shrinks and becomes flaccid in plant cells, the cell membrane tears away from the cell wall Plasmolysis - rupture of the membrane occurs, killing the cell Isotonic equal concentration of solute inside and outside of the cell EQUILIBRIUM Active Transport  the movement of particles from an area of low concentration to an area of high concentration (against the concentration gradient) uses ATP (cell energy) eg. a toxic substance outside of the cell will actively be pumped out eg. micronutrients need to be brought into the cell no matter how low the concentration is Carrier Proteins certain membrane proteins use ATP (cell energy) to change their shape, allowing particles to be taken in or out against natural diffusion Endocytosis the cell membrane folds around a substance, bringing it into the cell this folded membrane becomes a vacuole two types phagocytosis cell “eating” - taking in solids pinocytosis cell “drinking” - taking in liquids receptor-mediated endocytosis substances attach to membrane receptors this causes the membrane to fold inward creating a coated vessicle eg. LDL (cholesterol) uptake, glucagon, prolactin, insulin, GH, LH these are all hormones Exocytosis vacuoles containing wastes, to be removed or cell products (eg. proteins) for export the vacuole approaches the cell membrane, fuses with it, expelling the contents