Chemistry, Water, and Biochemsitry The Organic Molecules “You are what you eat!”

Biochemistry Preview/Review 90 naturally occurring elements on Earth’s crust 90 naturally occurring elements on Earth’s crust 11 are common to living organisms 11 are common to living organisms 20 found in trace amounts 20 found in trace amounts 4 elements make up approximately 96.3% of the total weight of the human body: 4 elements make up approximately 96.3% of the total weight of the human body: nitrogen nitrogen carbon carbon oxygen oxygen hydrogen hydrogen In varying combinations and amounts, these four elements make up mostly all of the compounds found in living things In varying combinations and amounts, these four elements make up mostly all of the compounds found in living things

Elements by Mass in the Human Body Oxygen: 65% Oxygen: 65% Carbon: 18.5% Carbon: 18.5% Hydrogen 9.5% Hydrogen 9.5% Nitrogen: 3.3% Nitrogen: 3.3% Phosphorus: 1.0% Phosphorus: 1.0% Sulfur 0.3% Sulfur 0.3% Sodium: 0.2% Sodium: 0.2% Magnesium: 0.1% Magnesium: 0.1% Silicon: trace Silicon: trace Fluorine: trace Fluorine: trace C.H.N.O.P.

Chemical Bonds: Hydrogen Bonds Hydrogen bonds are a type of weak chemical bond formed when the partially positive hydrogen atom participating in a polar covalent bond in one molecule is attracted to the partially negative atom participating in a polar covalent bond in another molecule or in another part of the same macromolecule

Properties of Water Water is unique in that it is the only natural substance that is found in all three states — liquid, solid (ice), and gas (steam) — at the temperatures normally found on Earth. Water is unique in that it is the only natural substance that is found in all three states — liquid, solid (ice), and gas (steam) — at the temperatures normally found on Earth.

Properties of Water   Water is a polar molecule.   A polar covalent bond is an attraction between atoms that share electrons unequally because the atoms differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it partially positive.

Properties of Water   Water freezes at 0 o C (32 o F) and boils at 100 o C (212 o F) at sea level, (but 186.4° at 14,000 feet). In fact, water's freezing and boiling points are the baseline with which temperature is measured.   Water is unusual in that the solid form, ice, is less dense than the liquid form, which is why ice floats.   Water expands upon freezing. Water molecules is an ice crystal are spaced relatively far apart because of hydrogen bonding. Floating ice insulates the water below and prevents seas and lakes from freezing solid.

Properties of Water Water has a high specific heat index. Hydrogen bonds absorb heat when they break, and release heat when they form, minimizing temperature changes. Water has a high specific heat index. Hydrogen bonds absorb heat when they break, and release heat when they form, minimizing temperature changes. This means that water can absorb a lot of heat before it begins to get hot. This is why water is valuable to industries and in your car's radiator as a coolant. This means that water can absorb a lot of heat before it begins to get hot. This is why water is valuable to industries and in your car's radiator as a coolant. The high specific heat index of water also helps regulate the rate at which air changes temperature, which is why the temperature change between seasons is gradual rather than sudden, especially near the oceans. The high specific heat index of water also helps regulate the rate at which air changes temperature, which is why the temperature change between seasons is gradual rather than sudden, especially near the oceans.

Properties of Water  Water has a very high surface tension. Hydrogen bonds hold molecules together. Water is sticky and elastic, and tends to clump together in drops rather than spread out in a thin film. Water is sticky and elastic, and tends to clump together in drops rather than spread out in a thin film. Surface tension is responsible for capillary action, which allows water (and its dissolved substances) to move through the roots of plants and through the tiny blood vessels in our bodies. Surface tension is responsible for capillary action, which allows water (and its dissolved substances) to move through the roots of plants and through the tiny blood vessels in our bodies.  Adhesion: The attraction between different kinds of molecules.  Cohesion: The attraction between molecules of the same kind.  Cohesion theory of water transport. Theory that the collective cohesive strength of their hydrogen bonds allows water molecules to be pulled up through a plant’s xylem in response to transpiration (evaporation of water) from leaves.

Properties of Water  Water has a high heat of vaporization. Hydrogen bonds must be broken for water to evaporate. Hydrogen bonds must be broken for water to evaporate. Evaporation of water cools the surfaces of plants and animals. Evaporation of water cools the surfaces of plants and animals. The heat of vaporization is the amount of heat energy needed to convert one gram of a liquid into a gas. The heat of vaporization is the amount of heat energy needed to convert one gram of a liquid into a gas.

Properties of Water Water has versatility as a solvent: Water has versatility as a solvent: Charged regions of polar water molecules are attracted to ions and polar compounds. Charged regions of polar water molecules are attracted to ions and polar compounds. Water is an effective medium for complex chemical reactions in organisms Water is an effective medium for complex chemical reactions in organisms A solution is a liquid consisting of a homogeneous mixture of two or more substances. A solution is a liquid consisting of a homogeneous mixture of two or more substances. A solvent is the dissolving agent. A solvent is the dissolving agent. A solute is the substance that is dissolved A solute is the substance that is dissolved

pH Water tends to disassociate into H + and OH - ions. In this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. Water tends to disassociate into H + and OH - ions. In this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. Pure water has the same number (or concentration) of H + as OH - ions, therefore the pH is 7 Pure water has the same number (or concentration) of H + as OH - ions, therefore the pH is 7 Acidic solutions have more H + ions than OH - ions. Acidic solutions have more H + ions than OH - ions. Basic solutions have less H + ions than OH - ions. Basic solutions have less H + ions than OH - ions. An acid causes an increase in the numbers of H + ions and a base causes an increase in the numbers of OH - ions. An acid causes an increase in the numbers of H + ions and a base causes an increase in the numbers of OH - ions.

pH The pH scale is a logarithmic scale representing the concentration of H + ions in a solution. The pH scale is a logarithmic scale representing the concentration of H + ions in a solution. If we have a solution with one in every ten molecules being H+, we refer to the concentration of H + ions as 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes Conversely 1/100 becomes 10 -2, 1/1000 becomes , etc. If we have a solution with one in every ten molecules being H+, we refer to the concentration of H + ions as 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes Conversely 1/100 becomes 10 -2, 1/1000 becomes , etc. Logarithms are exponents to which a number (usually 10) has been raised. The log 1/10 (or ) Logarithms are exponents to which a number (usually 10) has been raised. The log 1/10 (or ) pH, a measure of the concentration of H+ ions, is the negative log of the H + ion concentration. pH, a measure of the concentration of H+ ions, is the negative log of the H + ion concentration. If the pH of water is 7, then the concentration of H+ ions is 10 -7, or 1/10,000,000. If the pH of water is 7, then the concentration of H+ ions is 10 -7, or 1/10,000,000.

pH

What is polymerization? The formation of larger compounds from smaller compounds The formation of larger compounds from smaller compounds

The bonding process Polymers formed from monomers via dehydration synthesis Polymers formed from monomers via dehydration synthesis Where water is removed from the two joined molecules Where water is removed from the two joined molecules Separated via hydrolysis Separated via hydrolysis Where water is put back in place Where water is put back in place

Dehydration Synthesis A + B + C = ABC + 2 molecules of H 2 O H2OH2OH2OH2O

Hydrolysis ABC + 2 molecules of H 2 O = A + B + C In order to reverse the previous reaction (dehydration synthesis), we need to add water to the product ‘ABC’. So:

Example of a Modular Home (i.e., Macromolecule) Living Room Bed Room KitchenBathroom Monomers All of the individual monomers form the single polymer

So What’s In The Foods You Eat? Fats (a.k.a.- Lipids) Proteins Carbohydrates

Organic v. Inorganic Compounds? Contain carbon to hydrogen (C-H) bonds Contain carbon to hydrogen (C-H) bonds Inorganic compounds = NO (C-H) bonds Inorganic compounds = NO (C-H) bonds “Bucky Ball”

Compounds of Life: The Macromolecules There are four groups of organic macromolecules: There are four groups of organic macromolecules: Carbohydrates Carbohydrates Sugars, Starches Sugars, Starches Lipids Lipids Fats, Waxes, Oils Fats, Waxes, Oils Proteins Proteins Amino acids Amino acids Nucleic acids Nucleic acids RNA, DNA RNA, DNA

Carbohydrates Commonly referred to as sugars and starches Commonly referred to as sugars and starches Energy stored in the bonds of the carbohydrate molecule Energy stored in the bonds of the carbohydrate molecule 1 grams = 4 calories (Kilocalorie) 1 grams = 4 calories (Kilocalorie) Bonds easily broken down (water) by the body so “Carbs” are the body’s First Choice of Energy! Bonds easily broken down (water) by the body so “Carbs” are the body’s First Choice of Energy!

Carbohydrates They consist of Carbon, Hydrogen and Oxygen atoms in a consistent ratio of 1:2:1 or C 1 H 2 O 1 They consist of Carbon, Hydrogen and Oxygen atoms in a consistent ratio of 1:2:1 or C 1 H 2 O 1 The simplest unit/monomer: monosaccharides The simplest unit/monomer: monosaccharides

Monosaccharides Simple Sugars Simple Sugars Some examples are glucose, galactose and fructose Some examples are glucose, galactose and fructose They all have the same chemical formula, C 6 H 12 O 6, but they have different molecular structures They all have the same chemical formula, C 6 H 12 O 6, but they have different molecular structures Called Isomers Called Isomers

Monosaccharide Isomers

Forming Carbohydrate Polymers Two monosaccharides: glucose & fructose Two monosaccharides: glucose & fructose Form a disaccharide: Sucrose (Table Sugar) Form a disaccharide: Sucrose (Table Sugar) Put table sugar in a pan and turn on the heat…what happens? Put table sugar in a pan and turn on the heat…what happens?

Disaccharide formation GlucoseFructose C 6 H 12 O 6 + OH O + H2OH2O Sucrose C 12 H 22 O 11 Water formed from bond between two -OH structures with an ‘O’, remaining at bond

Disaccharides Other disaccharides are: Other disaccharides are: Maltose (malt sugars) Maltose (malt sugars) Lactose (milk sugars) Lactose (milk sugars) “Di-” & “Poly-” are “complex carbs” “Di-” & “Poly-” are “complex carbs” “Mono-” are “simple sugars” “Mono-” are “simple sugars”

Reversing Disaccharide formation with Hydrolysis O Sucrose C 12 H 22 O 11 + H2OH2O OH GlucoseFructose C 6 H 12 O 6 Add Water to Reaction

Function of Polysaccharides Polysaccharides are many (3 or more) monosaccharides joined together Polysaccharides are many (3 or more) monosaccharides joined together This is the form of sugar that is stored in living things This is the form of sugar that is stored in living things

Storage forms of Polysaccharides Glycogen is the animal form of stored sugar It can be hundreds to thousands of glucose molecules long It also shows a distinctive “branching” pattern Starch is the plant form of stored sugar It can be hundreds to thousands of glucose molecules long It does not “branch” like glycogen

Starches continued Cellulose is a type of starch that plants synthesize Cellulose is a type of starch that plants synthesize It is the principal component of wood, or the cell walls of plants It is the principal component of wood, or the cell walls of plants The human appendix is believed to have been used to break down cellulose tens of thousands of years ago The human appendix is believed to have been used to break down cellulose tens of thousands of years ago Humans, as a whole, can no longer break down cellulose and so it is now considered fiber in our diets Humans, as a whole, can no longer break down cellulose and so it is now considered fiber in our diets

Lipids Lipids include Lipids include fats, fats, oils oils waxes waxes **(Fats and waxes are solids at room temperature while oils are not) Lipids have three main functions: Lipids have three main functions: Energy storage Energy storage Forming biological membranes (cell membranes) Forming biological membranes (cell membranes) Chemical messengers in the body Chemical messengers in the body

Lipids Energy Storage: Potential Energy Energy Storage: Potential Energy

Lipids Biological Membranes: Cell Membranes Biological Membranes: Cell Membranes

Lipids Chemical Messengers: i.e., Steroids Chemical Messengers: i.e., Steroids

Lipids Cholesterol…Good or Bad?

Polymerization of a Lipid + H 2 O Glycerol Fatty Acid Chain Carboxyl

Saturated v. Unsaturated Fats Saturated Fats: No openings; Hydrogen bonded to every Carbon. Strong, hard to break bonds. LARD or CRISCO! Unsaturated Fats: Openings via Carbon to Carbon double bonds Bonds now easier to metabolize. CANOLA OIL, FISH OIL, ETC.

Proteins Proteins contain N, O, H and C Proteins contain N, O, H and C Proteins are made from long “chains” of amino acids Proteins are made from long “chains” of amino acids Bonds between amino acids called peptide bonds. Bonds between amino acids called peptide bonds. Proteins also called polypeptides. Proteins also called polypeptides. Amino acids have the same basic structure with the exception of the “R” group: LEGO! Amino acids have the same basic structure with the exception of the “R” group: LEGO!

Amino Acid Uses Proteins used for building and maintenance of tissues: i.e., muscle Proteins used for building and maintenance of tissues: i.e., muscle Not natural Natural

Amino Acid Uses Proteins (amino acid chains) are your last resort as a food source because they are difficult to metabolize Proteins (amino acid chains) are your last resort as a food source because they are difficult to metabolize

Amino Acid Structure Carboxyl Group Carbon Backbone w/”R” group Amino Group

Forming a Polypeptide through Dehydration Synthesis H2OH2O

The result of taking water from the two amino acids is a polymer, or protein, that has two monomers connected at a Carbon and a Nitrogen + H 2 O

Nucleic Acids 2 different nucleic acids: 2 different nucleic acids: RNA-Ribonucleic acid RNA-Ribonucleic acid DNA-Deoxyribonucleic acid DNA-Deoxyribonucleic acid Both are composed of: Both are composed of: Carbon Carbon Hydrogen Hydrogen Oxygen Oxygen Nitrogen Nitrogen Phosphorus Phosphorus

Nucleic Acids Monomers of nucleic acids are called nucleotides Monomers of nucleic acids are called nucleotides Nucleotides have three basic parts: Nucleotides have three basic parts: A special 5-carbon sugar A special 5-carbon sugar A phosphate group A phosphate group A nitrogenous base A nitrogenous base

Nucleic Acids The nitrogenous bases contain nitrogen The nitrogenous bases contain nitrogen A nucleotide, depending upon DNA on RNA, will have one of the following nitrogenous bases: A nucleotide, depending upon DNA on RNA, will have one of the following nitrogenous bases: Adenine (A) Adenine (A) Thymine (T) Thymine (T) Guanine (G) Guanine (G) Cytosine (C) Cytosine (C) Uracil (U) Uracil (U)

Diagram of a Nucleotide Phosphate Group 5-Carbon Sugar Nitrogenous Base