Bio chemistry notes
Water properties (as a result of hydrogen bonds)
-liquid rather than a gas at room temperature
-Having a high specific heat
-Having a high heat of vaporization
-Serving as a powerful solvent of polar molecules
-adhesion
-cohesion
-Being lighter as a solid than as a liquid
-Hydrophobic exclusion
Cohesion
Attraction between water molecules
Adhesion
Attraction between water molecules and other molecules (water has greater adhesion than cohesion)
Buoyancy
Living organisms have an overal density that is close to that of water, making it easy for them to live in aquatic environments
Viscosity
hydrogen bonds cause internal friction so pure water has a higher viscosity than organic solvents, and solutes increase the viscosity even further
Water potential
-measure of potential energy per unit volume
Absolute water potential cannot be easily measured so measurements are made relative to pure water energy at atmospheric pressures at 20 degress C
-Usually measured in kPa
-Always a negative value, because the solutes attract water molecules, making it harder for them to move
Water potential formula
Water potential = Pressure portential + solute potential
Top 4 macromolecules of living organisms
-Carbohydrates
-Lipids
-Proteins
-Nucleic acids
Carbohydrates
-Contains C, H, O
-Most abundant category of molecule in living things
-Includes sugars, starches, cellulose and chitin (pronounced kai-tin)
Functions are:
-Immediate energy source
-Energy storage
-Structural materials
Sugars
-Carbohydrates
-Immediate energy
-Simplest carbohydrates
-Monosaccharides and disaccharides
-Typically for rings in solutions
Monosaccharides
-General fromula of C(x)(H2O)(x)
-Classified as an aldose (aldehyde sugar) or ketose (ketone sugar) depending on the postion of the carbonyl group
-Also contians many hydroxyl (-OH) groups
-Polar, therefore soluble in water
Some examples of hexose sugars
-Glucose
-Galactose
-Fructose
Disaccharides
-Two monosaccharides joined by a glycosidic linkage
-The reaction that results in the glycosidic linkage is called a condensation reaction
Polysaccharides
-Many repeating monosaccharides (often a few hundred to a few thousand)
Can be broke down by hydrolysis reaction
-Either for storage or structure
Storage Polysaccharides (2 examples)
Starch
-Found in plants, used for energy storage
-Low solubility
-Made up of glucose monomers
Glycogen
-Found in animals, especially in the liver and muscles
-Extensively branched
Structural Polysaccharides (2 examples)
Cellulose
-Wood, paper, cotton
-Chief component of plant cell walls
-Long linear chains of glucose moleules joined by 1-4 linkages, with every second glucose upside down
-Each molecule has about 3000 glucose residues
-Many chains lie close together, held by hydrogen bonds from O to H on adjacent chains
-Produces a very rigid inflexible supporting structure
Chitin
-Found in the exoskeleton of arthropods as well as fungi
-Leathery becomes hardened when encrusted with calcium
-made of glucose residues with nitrogen-containing appendages
Lipids
Substances in a cell which are easily extracted by organic solvents; including fats, oils, waxes, steroids, and other large organic molecules.
Lipids (fats and oils - functions)
-Energy
-Cell membranes
-Hormones
-Insulation
-Protect organs from injury
-Store some vitamins
-Help conduct nerve impulses
Fatty acids
A long hydrocarbon chain and a carboxylic acid group
-Can be broken down to produce more than wice as much usable energy as glucose (weight for weight)
-Stored in the cytoplasm of many cells in the form of droplets of triglyceride molecules
Triglycerides
3 fatty acids chains joined to a glucerol molecule
Phospholipids
Two fatty acid chains instead of three, with the third potion on the glycerol occupied by a negatively charged phosphate group
Types of fats
unsaturated fats: good fats; mostly liquids at room temperature; mostly found in plants
Saturated fats; bad fats; mostly solid at room temperature, mostly found in animals
Trans fats: hydrogren on opposite sides of a double bond, unsaturated oil with cis bonds can be converted to trans by cooking
Proteins
-complex both in structure and function
-polymers of amino acids (polypeptides) that are then folded into a specfic conformation
Amino acids
-The buidling blocks of protiens
-20 different types
-Have an amino group and a carboxyl group
-The R group (reactive group) determines the characteristics of the amino acid
Amino group 2 Hs attached to an N - C (above attached to the H) (below atached to an R group) - Carboxylic group
Examples of amino acids
Tyrosine, Asparagine, Valine
Properties of the R side chains
Can be polar or nonpolar (hydrophillic or hydrophobic)
Basic or acidic
Fomation of polypeptides
Two amino acids are joined by the carboxyl group of one amino acid linking with the amino group of one other, this is called a dehydration reaction
Polypeptides are polar, with a carboxyl end and an amino end
Polypeptides that make up proteins can include thousands of amino acid monomers
Protein structure levels
The sequence of amino acids in the protein
Secondary structure
Fold and coils, held together by hydrogen bonds
Alpha helix or beta pleated sheet
Teritary structure
Contortions from bonding between side chains, often by hydrophobic interactions and disulfided bridges
Quaternary structure
Overal protein structure resulting from the aggregation of two or more polypeptide chains
Fibirous protein characteristics
-Long and narrow
-Insoluble
-Structural role
-ex myosin, collagen
Globular Protein Characteristics
-round
-soluble
-function over form, non structural
-haemoglobin, immunoglobin, insulin
Enzymes
Globular proteins that are catalysts of biological reactions, they accelerate the reactions without being used up in the process
Ways of classifiying reactions
Anabolic or catabolyic, anabolic builds (requires energy), catabolic breaks down (releases energy).
Intercellular or extracellular
Activation Energy
Energy required to break chemical bonds
Enzymes in relation to activation energy
Enzymes lower the activation energy needed for a reaction to take place
They do not change the overall free energy of a reaction, or whether the reaction is exergonic(releases energy) or endergonic(absorbs energy)
Substrate
The reactant that is acted on by the enzymes. Enzymes are typically very specific about the substate they recognize.
Active site
The region of the enzyme that recognizess and binds to the substrate
Lock and Key model
The substate fits into the enzyme, forming a reaction intermediate
Induced fit model
Wherein the enzyme changes structre slightly to adapt to the substrate, the enzymes is influenced and changed by the presence of the substrate
Regulation of enzyme activity
Temperature,
higher temperature, more kinetic energy, more collisions, more reaction, this balances out after a bit, too much heat will cause the intermolecular forces to be overcome
PH
Amino acids, which make up enzymes, are both acidic and basic, different ezymes have different PHs, a change in the PH of the envrionment could cause a reaction between the enzymes and their surroundings
Concentration of the substrate
increased concentration of the reactant will increase the rate of reaction, up to a plateau when all enzymes are saturated, aka occupied
Cofactors
Non protein compotent necessary for enzymes to function
Inhibtiors
Competitive inhibitors:
a chemical that resembles an enzymes substrate binds reversibly to the enzyme so that the enzyme is not available to the substrate
Non competitive inhibtiors (allosteric inhibition): a chemical binds to another part of the enzyme not the active site, causing it to change shape
Mechanism based inhibition
The irreversible binding of an inhibitor may causes chages to the active site of an enzyme
Ex penicillin
End product inhibition
a downstream product acts as an allosteric inhibitor to an earlier enzyme. This allows for regulation of the quantity of product formed in a biological reaction.
Denaturation of enzymes
When an enzymes sturcture is altered so it no longer is functional