CH 4: Biomolecules, Mar 11

Biomolecules

• Water makes up 60-70% of total body mass.

• Without water, people can live without water for 4-5 days before kidney failure occurs.

• People can live without food for 3-4 weeks as long as they have water.

1. POLARITY

• H2O, the hydrogen and oxygen atoms share electrons to form covalent bonds.

• These atoms do not share the electrons equally.

• Electronegativity is not equal.

• The oxygen atom has a greater ability to attract electrons than hydrogen.

• The electrons are closer to the oxygen than hydrogen.

• The oxygen atom has a partial negative charge,

1. HYDROGEN BONDING

• The polar nature of water also causes water molecules to be attracted to one another.

• The positively charged region of one water molecule is attracted to the negatively charged region of another water molecule.

• This attraction is called a hydrogen bond.

• Hydrogen bonds are weak and can break easily but also reform quickly.

2. SOLUBILITY OF WATER

• The polar nature of water allows it to dissolve polar substances, such as sugars, ionic compounds, and some proteins. 

• Water does not dissolve nonpolar substances, such as oil.

• Nonpolar substances have even electron distribution between atoms.

• There is a weaker attraction between polar and nonpolar molecules than between two polar molecules.

• Water dissolves the ionic compound sodium chloride, NaCl.

• Molecules that interact with water are called hydrophilic (polar molecules)

• Molecules that do not interact with water are called hydrophobic (nonpolar or non-ionized particles)

3. PROPERTIES OF WATER

1. Water is liquid at room temperature.

• Most compounds with a low mass are usually in a gas state at room temperature.

• Water is the exception due to hydrogen bonds.

• Eg. O2 has a mass of 16 amu x 2 = 32 amu and is liquid at room temp.

2. Water has polarity and helps with chemical reactions in our bodies.

• When ionic compounds are placed in water, the ions dissociate.

• Dissociation is when the ionic bonds are broken and ions are separated.

• This is due to the polarity of water that surrounds the ion.

• Water acts as a vehicle to facilitate reactions by bringing ions together.

• Ions that interact with water are hydrophilic (Na+)

• Ions that are non-ionized and nonpolar are hydrophobic (fats and oils)

3. Cohesion and Adhesion

1. Cohesion

• Cohesion is when water molecules stick to each other as a result of hydrogen bonding.

• Surface tension is when water acts as if it has a thin “skin” on its surface.

• Eg. Overfilling a drinking glass with water reveals a bulge above the rim of glass.

• Eg. Spiders and water striders run on water without breaking the surface.

• This allows blood to flow smoothly in our blood vessels.

• Also transports important substances throughout the body.

2. Adhesion

• Adhesion is the attractive force between two particles of different substances,

• Eg. water and glass. No matter how hard you shake the glass, water will always be attached.

• Cohesion and adhesion allows water to move upward against gravity from plant roots to their leaves.

4. Water changes temperature slowly

• Water has a high heat capacity, which means that water can absorb or release relatively large amounts of energy in the form of heat with only a slight change in temperature.

• This is due to hydrogen bonds

• Water prevents us from losing heat quickly.

• Water is a temperature buffer. (Resists changes)

5. Water has a high heat vaporization

• The H-bonds require energy to break.

• There are a lot of H-bonds in water so it can absorb a lot of energy or has a HIGH HEAT VAPORIZATION before it breaks and water boils and begins to evaporate. (Has a high boiling point, 100°C)

• Water holds onto this heat and acts as a temperature buffer to prevent sudden temperature changes.

• This allows the earth to regulate its temperature through oceans.

• This allows organisms to stay cool by releasing heat through sweat.

• The sweat also evaporates off your skin and cools it (eg. You feel cold when you get out of a pool)

6. Density of Ice

• Why does ice float while other solids sink?

• Objects more dense than water should sink, less dense things float.

• So ice is less dense than water. → pockets of air/crystal like matter.

• But according to the KMT, ice should be denser than water. So why isn’t it denser?

• Unlike most solids, which are denser than their liquids, solid water is less dense than liquid.

• This property is due to the shape of the water molecule and hydrogen bonding.

• The angle between the hydrogen atoms is quite wide so when water forms solid ice, the angles in the molecules cause ice crystals to have large amounts of open space.

• The open space lattice structure causes ice to have a larger volume and less density.

• Because ice floats on water, ice insulates the water below from the cold air, which allows fish and other aquatic creatures to survive under the icy surface.

Acids and Bases

1. Solutions

• A solution is a mixture in which one or more substances are uniformly distributed in another substance.

• Solutions can be mixtures of liquids, colids, or gases.

• Eg. plasma, the liquid part of blood is composed of many types of ions and large molecules, as well as gases, that are dissolved in water.

• A solute is a substance dissolved in the solvent. (Anything not water)

• The solvent is the substance in which the solute is dissolved. (usually water).

• A saturated solution is one in which no more solute can dissolve.

• Aqueous solutions is a more specific name given to solutes dissolved in water.

2. ACIDS AND BASES

1. Ionization of Water.

• As water molecules move about, they bump into one another.

• The collisions change the chemical structure of water in 2 steps.

• Step 1: H2O -> H+ + OH-

• Step 2: H+ + H2O -> H3O+

• The H3O+ ion is called a hydronium ion.

• Acidity or alkalinity(Base) is the measure of how many hydronium ions and hydroxide ions dissolved in a solution.

• Neutral solution: # Hydronium ions = # hydroxide ions.

• In high school, we simplify it by focusing on the concentration of hydrogen ions.

2. ACIDS

• Acidic Solution: # hydronium ions > # hydroxide ions

• Eg. Adding HCl to water = HCl -> H+ + Cl-

• Step 2: H+ + H2O -> H3O⁺

• Acids tend to have a sour taste and are highly corrosive.

3. BASES

• Alkaline or basic solution: # of hydronium ions < # hydroxide ions.

• Eg. Add NaOH to water = NaOH -> Na⁺ + OH^-

• Bases have a bitter taste and feel slippery.

• Slippery feeling is the OH^- ions reacting with oil on our skin to form soap.

• Commercial soap is the product of a reaction between a base and a fat.

4. Litmus

• In Science 10, you learned to use acid base indicators to determine the pH range of an unknown solution.

• Red and blue litmus paper was one of those indicators.

5. pH Scale

• Fish can’t swim in a pool of acid, plants can’t survive by watering it with acid. Thermoacidophiles can survive in acid.

• pH scale is used to measure acidity ranges from 0 to 14.

• In Chem 11, you will learn of a pH scale.

• Comes from latin “pondus hydrogenii” means hydrogen power of hydrogen potential.

• Is a measure of the concentration H3O+ in solution chemistry.

• pH of 0 is very acidic, a pH of 7 is neutral and a pH of 14 is very.

• pH is measured on a logarithmic scale. pH = -log[H⁺]

• Concentration measured in mol/L (M)

• Change of one pH unit reflects a 10-fold change in the acidity.

• If urine has pH 6 and water has pH 7, urine has 10 times more H3O+ ions than water.

6. Buffers

• pH is important of an environment can mean death or life for organisms

• Water = Temperature Buffer

• Enzymes can function only within a very narrow pH range.

• Buffers are used to control pH in organisms.

• Buffers are substances that neutralize small amounts of either an acid or a base added to a solution.

• Different parts of your body are basic and others are acidic.

• Acidic: Stomach and Urine

• Basic: Blood and intestines

• The main buffering agent in blood is carbonic acid.

• The main buffering agent in blood is carbonic acid (H2CO3) and hydrogen carbonate (HCO3-)

• The main job of the carbonic acid/bicarbonate system is to regulate body pH.

• When hydrogen ions (H+) are added to blood, the following reaction occurs:

• H+ + HCO3- -> H2CO3

• Kidneys are not the only system that can affect the buffer system.

• When hydroxide ions (OH-) are added to blood, this reaction occurs:

• OH- + H2CO3 -> HCO3- + H2O

• These reactions prevent any significant change in blood pH.

7. Bicarbonate Buffer Equation

• Exhaling CO2 also helps buffer against pH change. Needs to Memorize*

• le chatelier's principle → shifts to each side, Buffers balance

• CO2 + H2O ⇌ H2CO3 ⇌ HCO3- + H+, H2CO3 = Buffer

1. Metabolic Acidosis

• Keq: H2CO3- <-> H+ + HCO3-

• When Keq is reached, reaction “stops.”

• Metabolic Acidosis: H+ too high, pH too low, so there is a buildup of acid/H+ ions.

• LACTIC ACID FERMENTATION: results in shifting further to left, further to lungs, increasing rate of breathing.

• CO2 WORKS AS A STIMULANT FOR BREATHING

• Metabolic acidosis is the decrease in blood pH that results when excessive amounts of acidic substances are released into the blood.

• This can happen through prolonged over-exercising, diabetes, or restricted food intake.

• Normal body response is breathing out CO2

• Breathing raises pH level.

• Hydrogen ions have to be consumed with bicarbonate ions in order to produce CO2.

2. Metabolic Alkalosis

• Response: Eq shift to the right.

• Results from ingesting of vomiting, or through overuse of diuretics (make you pee)

• Lower and reestablish pH levels.

3. Respiratory Acidosis

• Stop breathing, shift to the right.

• CO2 increased, lungs only effect CO2 → decrease respiration rate. (asthma, pneumonia…)

4. Respiratory Alkalosis

• Increased breathing

• CO2 decreased

• Hyperventilation

• Fainting

• Response is for kidneys to excrete more bicarbonate, and release into blood more H+.

Organic Chemistry

Living things are based on the element carbon.

Carbon has the ability to form large and complex molecules.

1. CARBON COMPOUNDS

• Two categories: organic and inorganic compounds.

• Main backbone: Carbon

1. Inorganic

• Inorganic molecules are considered nonliving matter.

• Eg. NaCl, H2O

• They are still important to life processes

• Most do not contain carbon (there are a few exceptions).

2. Organic

• Organic molecules are considered living matter. Made in the body with structure base of Carbon

• Organic compounds are made primarily of carbon atoms and found in living organisms.

• A carbon atom has four electrons in its outermost energy level.

• Most atoms become stable when their outermost energy level contains eight electrons.

• Always 4 lines coming from carbon

• A carbon atom therefore readily forms covalent bonds with the atoms of other elements.

• Carbon can also readily bond with other carbon atom, forming straight chains, branched chains, or rings.

• This tendency of carbon to bond with itself results in an enormous variety of organic compounds.

• A bond formed when two atoms share one pair of electrons is called a single bond.

• A carbon atom can also share two or even three pairs of electrons with another atom.

• Carbon can also form double bonds (share two pairs of electrons) represented by two parallel lines atoms.

• Carbon can also form triple bonds, the sharing of three pairs of electrons, is represented by three parallel lines.

• Hydrocarbon chains can be built when carbons chain together

• Hydrogen is generally attached to carbon, exception: Functional Groups

• When other elements (functional groups) join onto the hydrocarbon chain, it creates a new organic molecule.

• FUNCTIONAL GROUPS

• Organic compounds are made of functional groups

• 4 important functional groups (main) are 

• 1) Hydroxyl -OH 

• 2) Carboxyl -COOH  

• 3) Amino -NH3 (NH2*)

• 4) Phosphate -PO4-

• These functional groups combine with hydrocarbon backbones to make amino acids.

• No functional group = happy compound.

• Hydrocarbon chains are hydrophobic (does not attach to water)

• Hydrocarbon chain with an ionized functional group is hydrophilic (can attach to water).

2. MACROMOLECULES

• Carbon compounds are built up from smaller, simpler molecules known as monomers.

• Monomers → polymers (combination of monomers).

• A polymer is a molecule that consists of repeated, linked units,

• Large polymers are called macromolecules.

• There are 4 main macromolecules each with its own unique monomer.

• There are 2 main chemical reactions for organic molecules.

1. Condensation Synthesis (Synthesis)

• Monomers link to form polymers through a chemical reaction.

• Each time a monomer is added to a polymer, a water molecule is created or synthesized.

2. Hydrolysis (Decomposition)

• Reverse of a condensation reaction where polymers break down into monomers.

• Water is used up to break the bond linking each monomer.

1. CARBOHYDRATES

• Generally used for energy

• Short term energy (eg. sugar) - good for sports. → Monomer

• Long term energy (rice, pasta, potatoes) - good for long endurance sports (marathons, boxing) → Polymers

• Molecules made up of hydrogen, carbon and oxygen.

• Seen as a general formula: C-H-OH, but in variety of different shapes

1. Simple Carbohydrates: Monosaccharides

• A monomer of a carbohydrate

• A monosaccharide – or simple sugar – contains C:H:O in,a ratio of 1:2:1

• The general formula is (CH₂O)n where n is any whole number from 3 to 8 → b/c its monosaccharides.

• Eg. a six-carbon monosaccharide, (CH₂O)₆, would have the formula C6H12O6.

• Ribose: 5 carbon or pentose (CH₂O)₅

• Glucose: 6 carbon or hexose sugar.

• Characterized by a -OH hydroxyl. → Sugars

• Characterized by a -OH hydroxyl group on the carbon ring.

• Common monosaccharides are: glucose, fructose, and galactose.

1. Glucose is a main source of energy for cells

2. Fructose is found in fruits and is the sweetest of the monosaccharides.

3. Galactose is found in milk.

• All 3 sugars have the same molecule formula, C6H12O6, but differing structures.

• The different structures determine the slightly different properties (ie. different tastes) of the three compounds.

• Compounds like these sugars, with a single chemical formula but different structural forms, are called isomers.

2. Disaccharides

• Monomer + Monomer <-> Polymer + H2O

• Monosaccharide + monosaccharide <-> disaccharide + H2O (More specific for carbs)

• Made of two monosaccharides joined together in a condensation reaction.

• Monosaccharides fructose and glucose can combine to form the disaccharide sucrose.

3. Polysaccharides

• If there are more than 2 sugars, it is called a polysaccharide.

• When animals eat or when plants photosynthesize, they create monomers of monosaccharides.

• They store monosaccharides as polysaccharides for long term storage.

• GLYCOGEN (Chains) → Intermediate energy, between monomer and polymer

• Animals store glucose in the form of the polysaccharide glycogen.

• Glycogen consists of hundreds of glucose molecules strung together in a highly branched chain.

• Much of the glucose that comes from food is ultimately stored in your liver and muscles as glycogen

• When we need energy, the liver and muscles break off monosaccharides from the glycogen to be converted into the energy molecule ATP.

• Plants store glucose molecules in 2 types of polysaccharide. → Starch

• A) Starch: Highly branched chains that are similar to glycogen.

• B) Cellulose: Unbranched coiled chains

• Cellulose, which gives strength and rigidity to plant cell walls, makes up about 50 percent of wood.

In a single cellulose molecule, thousands of glucose monomers are linked in long, straight, chains.

1. LIPIDS

• Has many different functions throughout the body:

1. Energy Storage. → Fat

2. Insulation of nerves and under the skin.

3. Structure for cell membranes (phospholipids)

• Lipids are large, nonpolar (no charge, polar = charge) organic molecules.

• Recall nonpolar molecules do not dissolve in water.

• Lipids include triglycerides, phospholipids, steroids, waxes, and pigments.

• Lipid molecules have more carbon-hydrogen bonds per gram so they store more energy per gram.

1. Fats and Oils

• Glycerol + 3 fatty acids <-> fat + 2 H2O.

• Glycerol has 3 and only 3 hydroxyl -OH groups.

• Fatty acids have a carboxyl group -COOH. (double bonded O)

• Fatty acids are unbranched carbon chains.

• Fats are called triglycerides because of their 3 part structure (3 fatty acid chains).

• 2 types of fatty acids.

1. Saturated Fatty acids

• Animal fats

• Main property: Solid at room temp

• Hydrocarbon chain are linked to hydrogen in single bonds.

• It can stack very well, carries a lot of flavour.

• Palmitic acid (peanut or coconut oil), butyric acid (butter).

• Cause of atherosclerosis (hardening and narrowing of heart arteries).

2. Unsaturated Fatty Acids:

• Vegetable oils

• Minimum of one carbon double bond = Unsaturated Fats

• Carbons form double bonds between carbons and have less hydrogens.

• Linoleic acid (omega 3 or omega 6 fats) - grapeseed, sunflower oil.

• They are soft or liquid at room temperature.

• Eg. plant seeds such as olive oil, canola oil where they serve as energy plants.

3. Trans fats

• There are two broad types of trans fats found in foods:
  A) Naturally occurring Trans Fats

  • Naturally occuring trans fats are produced in the gut of some animals and foods made from these animals (eg. milk and meat products) may contain small quantities of these fats.

B) Artificial Trans Fats

• Artificial trans fats (or trans fatty acids) are created in an industrial process.

• Adds hydrogen to liquid vegetable oils to make them more solid.

• Used by companies because it is cheap and tastes good.

• Raises LDL (low-density lipoprotein) cholesterol (bad cholesterol)

• Increase chances of strokes and heart disease.

• Increase chances of diabetes II.

• Found in red meat (beef, lamb), fried foods (donuts, fries)

2. Soaps

• Technically not a lipid or fat

• Inorganic base + fatty acid -> soap.

• Soap is hydrophilic & hydrophobic, can connect to water or fat.

• Soaps are great for removing oil from dishes because it can mix with both fats and water.

• Soaps have a polar end (hydrophilic that mixes with water) and nonpolar end (hydrophobic that mixes with fat).

• Emulsification: When fats are spread apart/dispersed in water (washing clothes or dishes).

• When you eat fatty foods, the fat is emulsified by bile.

• Bile → takes fat and separates it, polar and nonpolar end.

• Bile is made in the liver and stored in the gall bladder.

• The gall bladder releases bile into your intestines when you digest fatty foods.

• The gall bladder stores bile when you don’t eat (sleeping).

• If you suffer from gall stones and have your surgically removed.

• Without the gall bladder, bile constantly fills your intestine

• Too much bile acts as a laxative causing diarrhea.

• People without a gall bladder must change to a high fibre diet and low fat diet to avoid diarrhea.

3. Phospholipids

• Composed of two fatty acids and 1 phosphate group attached to glycerol.

• Cell membrane is made of two layers of phospholipids, called the lipid bilayer.

• The inability of lipids to dissolve in water allows the membrane to form a bilayer.

• 2 fatty acid tails attached to a polar group/ nitrogen

• Hydrophilic Head and Hydrophobic tail (2 tails)

• The two ends of the fatty acid molecule have different properties.

• The phosphate nitrogen end is polar and is thus hydrophilic or attracted to water molecules.

• In contrast, the hydrocarbon end of the fatty-acid molecule is nonpolar or hydrophobic so it does not interact with water.

4. Steroids

   1. Composed of cholesterol: four fused carbon rings with various functional groups attached to them

   2. Cholesterol is the basic structure for other hormones 

      1. E.g. male hormone testosterone, female hormone estrogen 

   3. Cholesterol is also a component of the cell membrane 

   4. Bad cholesterol or LDLs (low density lipoprotein) deposits cholesterol in arteries leading to stroke and heart attacks 

   5. Good cholesterol or HDLs (high density lipoprotein) take cholesterol away from arteries (check later) 

Proteins

• Found in meats (beef, chicken, fish) 

• Almost everything is made up of protein

• Found in vegetables (beans, lentils, quinoa) 

• Two Functions 

1. Structural 

   1. Makes things like hair, skin, muscles, collagen 

2. Enzymes  

   1. Speeds body chemical reactions 

      1. E.g. Digesting foods 

Amino Acids

• Proteins are formed from the linkage of monomers called amino acids 

• Amino acids are classified into three groups: 

1. ESSENTIAL AMINO ACIDS 

   1. Essential amino acids cannot be made by the body 

   2. As a result, they must come from food (External Source)

   3. There are 9 essential amino acids 

2. NON-ESSENTIAL AMINO ACIDS 

   1. Nonessential means that our bodies produce an amino acid even if we do not get it from the food we eat 

   2. There are 11 non-essential amino acids 

3. CONDITIONAL AMINO ACIDS 

   1. Conditional amino acids are non-essential amino acids that become essential during times of illness and stress (sacrifices these conditionally amino acids)

There are 20 different amino acids, and all share a basic structure