Chapter 2
Chemical basis of life
chemicals compose the structures of the body, and the interactions of chemicals with one another are responsible for the functions of the body.
Basic chemistry
Atomic Structure
1. Subatomic particles that compose atoms:
a. proton 1 positive charge
b. neutron neutral or no charge
c. electron 1 negative charge
i. the positive charge of the proton is equal in magnitude to the negative charge of the electron
ii. the numbers of protons and electrons in each atom is equal
iii. the charges cancel each other out
iv. an atom is electronically neutral
2. nucleus formed by protons and neutrons
a. accounts for 99.97% of an atoms weight
b. only 1 ten-trillionth of its volume
3. electron cloud the region where any given electron is located at any particular moment
a. likelihood of locating an electron at a specific point in a region correlates with the darkness of that region
b. the darker the color, the greater the likelihood of finding the electron there at a given moment
Atomic number and Mass number
Isotopes and atomic mass
i. Hydrogen 1 proton, 1 electron, no neutrons
ii. Deuterium 1 proton, 1 electron, 1 neutron
iii. Tritium 1 proton, 1 electron, 2 neutrons
i. Hydrogen 1H,
ii. Deuterium 2H
iii. Tritium 3H
Electrons and chemical bonding
1. Chemical bonding: the outermost electrons of an atom determine its chemical behavior. When they are transferred or shared between atoms, chemical bonding occurs.
a. two major types
2. ionic bonding
a. if an atom loses or gains electrons, the number of protons and electrons are no longer equal creating a charged particle an ion
b. if it loses an electron, this makes the atom be positively charged like sodium -- cations
c. if the atom gains an electron, this makes the atom be negatively charged like chloride anions
d. opposites attract and cations and anions stay close together in iconic bonding
e. sodium and chloride ions are held together this way to form sodium chloride -- salt
3. covalent bonding results when atoms share one or more pairs of electrons
a. resulting combo of atoms is called a molecule
b. 2 hydrogen atoms form a covalent bond to form a hydrogen molecule
c. The positively charged nucleus of each hydrogen atom attract the electron of the other atom.
d. At an optimal distance the 2 nuclei mutually attract the 2 electrons, and each electron is shared by both of them. Theyre not held by a covalent bond
4. single covalent bond
a. an electron pair is shared between 2 atoms
b. represented by a single line between the symbols of the atoms involved
c. HH (hydrogen)
5. double covalent bond
a. results when 2 atoms share 4 electrons
b. 2 from each atom
c. Represented by a single line between the symbols of the atoms involved
d. O==C==O (carbon dioxide)
6. nonpolar covalent bonds
a. electrons are shared equally between atoms i.e. hydrogen molecule
7. polar covalent bonds
a. do not share their electrons equally between atoms
b. the nucleus of one atom attracts the electrons more strongly than the other
c. common in living and non-living matter
d. can result in polar molecules which are electronically asymmetric
i. oxygen atoms attract electrons more strongly than hydrogen atoms
ii. in a water molecule, the electrons are located nearer the oxygen nucleus
iii. the electrons have a negative charge making the oxygen side of the molecule slightly more negative than hydrogen side
Molecules and Compounds
i. theyre held together by force of attraction
ii. sodium chloride is a compound but not a molecule
Intermolecular forces
1. intermolecular forces
a. result from weak electrostatic attractions between the oppositely charged parts of molecules
b. or between ions and molecules
c. weaker than the forces producing chemical bonding
2. hydrogen bonds
a. molecules with polar covalent bonds have positive and negative ends the oppositely charged ends are attracted to each other
b. when the positively charged hydrogen of 1 molecule is attracted to the negatively charged oxygen, nitrogen, or fluorine of another molecule
c. positive charged hydrogen atoms of water molecule form hydrogen bonds with the negatively charged oxygen atoms of another water molecule
d. important in determining shape of complex molecules
e. provides a cohesiveness
3. solubility the ability of one substance to dissolve in another
a. i.e. sugar dissolves in water
b. charged substances (sodium chloride) and polar substances (glucose) dissolve in water readily
c. non polar substances such as oils do not
d. substances dissolve when surrounded by water molecules and the positive and negative ends of the water molecules are attracted more to the charged ends of the other molecule than they are to each other
e. the hydrogen bonds in the water molecule are broken and the water molecules then surround the other molecules which become dissolved
f. most molecules (covalent compounds) remain intact even though surrounded by water molecules
4. dissociate (separate)
a. when iconic compounds dissolve in water their ions separate from each other
b. the cations are attracted to the negative ends of the water molecules
c. the anions are attracted to the positive ends of the water molecules
d. the sodium and the chloride ions separate and the water molecules surround and isolate them keeping them in solution
5. electrolytes
a. cations and anions that dissociate in water
b. they have the capacity to conduct an electric current the flow of charged particles
c. ECG is a recording of the electric currents produced by the heart
6. nonelectrolytes molecules that do not dissociate
a. form solutions that do not conduct electricity
b. pure water is a nonelectrolyte
Chemical reactions and Energy
Types of chemical reactions
i. water is removed from the amino acids as they are bound together
i. water must be split into two parts and each part contributed to one of the new glucose molecules
ii. hydrolysis reactions -- use water in this way
i. i.e. from food
i. i.e. muscle contractions
Inorganic chemistry
i. Water has a high specific heat meaning a relatively large amount of heat is required to raise its temperature. Therefore it resists large temperature fluctuations
ii. when water evaporates, heat is required
iii. the evaporation of water from the surface of the body gets rid of excess body heat
i. water is an effective lubricant for protection from friction damage
ii. tears protect the eye from the eyelid
iii. forms a cushion around organs to protect them from trauma
iv. i.e. cerebrospinal fluid surrounds brain
i. many chemical reactions necessary for life do not take place unless the reacting molecules are dissolved in water
ii. sodium chloride must dissociate in water into Na+ and Cl- before they can react with other ions
iii. water directly participates in many chemical reactions
iv. dehydration reaction is synthesis reaction that produces water
v. hydrolysis reaction is a decomposition reaction that requires a water molecule
i. Mixture a combination of two or more substances physically blended together, but not chemically combined.
ii. Solution any mixture of liquids, gases, or solids in which the substances are uniformly distributed with no clear boundary between the substances.
1. the solute dissolves in the solvent
2. water is the solvent and salt the solute in a salt solution
iii. suspension a mixture containing materials that separate from each other unless they are continually, physically blended together
1. blood is a suspension liquid containing red blood cells suspended in liquid (plasma)
2. it will separate into layers if allowed to sit
iv. colloid a mixture in which a dispersed (solutelike) substance is distributed throughout a dispersing (solventlike) substance
1. the dispersed particles are larger than a simple molecule but small enough that they remain dispersed and do not settle out
2. proteins which are like large molecules and water form colloids
a. plasma and the liquid portion of cells are colloids containing many important proteins
Acids and Bases
i. They release almost all of their H+ or OH- (hydrogen or hydroxide)
ii. The more completely the acid or base dissociates, the stronger it is
iii. HCl is a strong acid because it completely dissociates in water
i. They release only some of their H+ or OH-
ii. Acetic acid when dissolved in water, some dissociates but some remains in undissociated form. An equilibrium is established between the ions and undissociated weak acid
iii. For a weak acid or base, the amount of dissociated ions relative to the weak acid or base is a constant
iv. Vinegar is a weak acid
i. Solution with PH of 6 has H+ concentration 10 times greater than a solution with PH of 7 and 100 times greater than a solution with PH of 8
i. Acidosis blood PH drops below 7.35
1. nervous system is depressed
2. person can become disoriented and possibly comatose
ii. Alkalosis blood PH rises above 7.45
1. nervous system is overexciteable
2. person can be extremely nervous or have convulsions
i. buffer is a solution of a conjugate acid-base pair in which the acid component and the base component occur in similar concentrations
ii. a conjugate base is everything that remains of an acid after the H+ (proton) is lost
iii. a conjugate acid is formed when a H+ is transferred to the conjugate base
iv. carbonic acid (H2CO3) and a bicarbonate ion (HCO3-) formed by the dissociation of H2CO3 are a conjugate acid-base pair
Oxygen (O2)
a. is an organic molecule consisting of two oxygen atoms bound together by a double covalent bond.
b. 21% of the gas in the atmosphere is oxygen and is essential for most animals
c. Required by humans in the final step of a series of reactions in which energy is extracted from food molecules
Carbon Dioxide (CO2)
a. consists of two oxygen atoms bound to one carbon atom.
b. Each oxygen atom is bound to the carbon atom by a double covalent bond
c. CO2 produced when organic molecules such as glucose are metabolized within the cells of the body
d. The energy stored in the covalent bonds is transferred to other organic molecules when glucose is broken down
e. CO2 is a metabolic by product, transferred to lungs by blood, and exhaled during respiratioin
f. CO2 build up in cells can be toxic
Organic Chemistry
The ability of carbon to form covalent bonds with other atoms makes possible the formation of the larger, diverse, complicated molecules necessary for life.
The backbone of large molecules
4 major groups: carbohydrates, lipids, proteins, and nucleic acids
Carbohydrates
i. glucose, fructose, and galactose
ii. molecules that have the same number and types of atoms but differ in their 3D arrangement
iii. glucose blood sugar the major carbo found in the blood and is major nutrient for most cells of the body
i. ribose and deoxyribose
ii. both components of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), respectively
i. Important energy storage molecule
ii. Can be metabolized rapidly and the resulting energy can be used by cells.
iii. Substantial amount is metabolized to produce energy during exercise and stored in the cells of the liver and skeletal muscles
i. 2 important polysaccharides found in plants
ii. Both composed of long chains of glucose
iii. Starch is broken down and used as energy
iv. Cellulose is not broken down because humans dont have the necessary digestive enzymes eliminated in feces
Lipids
1. Lipids
a. composed primarily of carbon, hydrogen, and oxygen
b. less polar due to a lower ratio of oxygen to carbon
c. relatively insoluble in water
2. roles of lipids in the body
a. protection fat pads surround vital organs
b. insulation fat under skin prevents heat loss. myelin surrounds nerve cells and electrically insulates the cells from one another
c. regulation steroid hormones regulate many physiologic processes
i. estrogen and testosterone are sex hormones responsible for many differences between male and female
ii. prostaglandins help regulate tissue inflammation and repair
d. vitamins fat soluble vitamins perform variety of functions
i. vitamin A forms retinol which is necessary for seeing in the dark
ii. active vitamin D promotes calcium uptake in the small intestine
iii. vitamin E promotes wound healing
iv. vitamin Kathryn necessary for the synthesis of protein responsible for blood clotting
e. structure phospholipids and cholesterol are important components of plasma membranes
f. energy lipids can be stored and broken down later for energy
i. per unit of weight, they yield more energy than carbos or proteins
3. Fats major type of lipid
a. fats are ingested and broken down by hydrolysis reactions in cells to release energy for use by those cells
b. stored for later use if needed
c. protection by padding organs and preventing heat loss
4. triglycerides constitute 95% of the fats in the body
a. sometimes called triacylglycerols
b. consist of 2 different types of building blocks 1 glycerol and 3 fatty acids
c. glycerol 3 carbon molecules with a hydroxyl group attached to each carbon atom
d. fatty acids consist of a straight chain of carbon atoms with a carboxyl group attached at one end
e. carboxyl group consists of both an oxygen atom and a hydroxyl group attached to a carbon atom
i. responsible for acidic nature of the molecule because it releases hydrogen ions into solution
5. Glycerides described according to number and kinds of fatty acids that combine with glycerol through dehydration process
a. Monoglycerides have 1 fatty acid
b. Diglycerides have 2 fatty acids
c. Triglycerides have 3 fatty acids
6. Fatty acids
a. differ from one another according to the length and degree of saturation of their carbon chains
b. most naturally occurring fatty acids have an even number of carbon atoms
c. 14 to 18 carbon chains being the most common
d. Saturated fatty acid contains only single covalent bonds between the carbon atoms
i. Sources include: beef, pork, whole milk, cheese, butter, eggs, coconut oil, and palm oil
e. Unsaturated fatty acid the carbon chain is unsaturated if it has 1 or more double covalent bonds between carbon atoms
i. Double bonds can occur anywhere along the carbon chain so many types of unsaturated fatty acids with an equal degree of unsaturation are possible
1. Monounsaturated fats olive oil and peanut oil have one double covalent bond
2. polyunsaturated fats safflower, sunflower, corn, or fish oils have 2 or more double covalent bonds
ii. the best type of fats in the diet because they do not contribute to development of cardiovascular disease
7. Phospholipids
a. Similar to triglycerides, except one of the fatty acids bound to the glycerol is replaced by a molecule containing phosphate and usually nitrogen
b. Important structural components of the plasma membranes
c. Polar at the end of to which the phosphate is bound
d. Non polar at the other
e. Polar end attached to water and said to be hydrophilic (water loving)
f. Non polar end repelled by water and said to be hydrophobic (water fearing)
8. eicosaniods a group of important chemicals derived from fatty acids
a. made in most cells and are important regulatory molecules
b. they have a role in response of tissues to injuries
c. prostaglandins may be involved in regulating secretion of some hormones, blood clotting, some reproductive functions, and other processes
d. aspirin and other anti-inflammatory drugs have an ability to inhibit prostaglandin synthesis
e. eicosanoids include:
i. prostaglandins
ii. thromboxanes
iii. leukotrines
9. steroids
a. differ in chemical structure from other lipid molecules but their solubility characteristics are similar
b. all steroid molecules are composed of carbon atoms bound together in to 4 ringlike structures
c. important steroids
i. cholesterol
1. important component of plasma membrane
2. a certain amount is vital for normal functions
3. high levels can increase risk of cardiovascular disease
ii. bile salts
iii. estrogen
iv. progesterone
v. testosterone
10. fat soluble vitamins
a. Structures not closely related to one another but they are nonpolar molecules essential for normal functions of the body
Proteins
1. Proteins
a. all proteins contain carbon, hydrogen, oxygen, and nitrogen bound by covalent bonds. Most contain some sulfur as well.
b. most are very large and complex molecules
c. tend to form collids and not solutions
d. proteins are polypeptides composed of hundreds of amino acids
2. role of proteins in body
a. regulate body processes
i. enzymes control chemical reactions
ii. hormones regulate may physiologic processes
1. insulin affects glucose transport into cells
b. act as transportation system
i. hemoglobin transports oxygen and carbon dioxide in the blood
ii. plasma proteins transport many substances in the blood
iii. proteins in the plasma membranes control the movement of materials into and out of the cell
c. provide protection
i. antibodies and complement protect against microorganisms and other foreign substances
d. help muscles contract
i. actin and myosin in muscle are responsible for muscle contraction
e. provide structure
i. collagen fibers form a structural framework in many parts of the body
ii. keratin adds strength to skin, hair, and nails
f. provide energy
i. proteins can be broken down for energy
ii. per unit of weight they yield as much energy of carbos
3. protein structure
a. basic building blocks are the 20 amino acid molecules
b. each amino acid has an amine group, a carboxyl group, a hydrogen atom, and a side chain designated by the symbol R attached to the same carbon atom
c. the side chain can be a variety of chemical structures
d. differences in the side chains make the amino acids different from each other
4. peptide bonds
a. covalent bonds formed between amino acids during protein synthesis
b. dipeptide 2 amino acids bound together by a peptide bond
c. tripeptide 3 amino acids bound together by peptide bonds
d. polypeptide many amino acids bound together by peptide bonds
e. proteins are polypeptides composed of hundreds of amino acids
5. primary structure of a protein is determined by the sequence of the amino acids bound by the peptide bonds
a. potential number of different proteins is huge because the 20 amino acids can be located at any position along a polypeptide chain
b. characteristics of the amino acids in a protein determine the 3D shape of the protein and the shape of the protein determines its function
c. changing 1 or a few of the amino acids in a primary structure can alter protein functions making it less or even non functional
6. secondary structure results from the folding or bending of the polypeptide chain caused by the hydrogen bonds between amino acids.
a. 2 common types
i. Helices coils
ii. Pleated sheets folded sheets
b. If the hydrogen bonds are broken, the protein becomes non functional
c. Denaturation the change of the shape
i. Can be caused by high temp
ii. Changes in PH of body fluids
iii. Egg whites cooked is a good example
7. tertiary structure results from folding of the helices or pleated sheets
a. some acids are very polar and form hydrogen bonds with water
b. polar portions of proteins tend to remain unfolded, maximizing their contact with water
c. the less polar portions tend to fold into globular shape, minimizing their contact with water
d. formation of covalent bonds between sulfur atoms of 1 amino acid and sulfur atoms in another amino acid located at a different place in the sequence can also contribute to the tertiary structure
e. tertiary structure determines the shape of a domain, which is a folded sequence of 100 to 200 amino acids within a protein
f. the function of proteins occur at 1 or more domains
g. changes in the primary or secondary structure that affect the shape of the domain can change protein function
8. subunits 2 or more proteins associate to form a function unit
9. quaternary structure refers to the spatial relationships between the individual subunits
Enzymes
i. Lipase enzyme that catalyzes the breakdown of lipids
ii. Protease enzyme that breaks down proteins
i. Some control enzyme concentration by influencing rate at which the enzymes are synthesized
ii. Some alter the activity of existing enzymes
iii. Much of what is known about regulation of cellular activity involves knowledge of how enzyme activity is controlled
i. sensitive to PH and temp which can break their hydrogen bonds
ii. breaking the hydrogen bonds changes the relationship between the amino acids, making a change in shape, and that prevents the enzyme from functioning properly
Nucleic Acids DNA and RNA
1. Deoxyribonucleic acid (DNA)
a. is the genetic material of cells and copies are transferred from one generation of cells to the next
b. contains the info that determines the structure of the proteins
2. Ribonucleic acid (RNA)
a. Structurally related to DNA
b. 3 types play important roles in synthesis
3. Nucleic acids large molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus
4. nucleotides
a. composed of a monosaccharide to which a nitrogenous organic base and a phosphate group are attached
i. 5 carbon monosaccharide deoxyribose for DNA
ii. 5 carbon monosaccharide ribose for RNA
b. Nitrogenous organic bases
i. Consist of carbon and nitrogen atoms organized into rings
ii. Bases because the nitrogen atoms tend to take up H+ from solution
iii. The nitrogenous organic bases are thymine, cytosine, and uracil all single ringed pyrimindines. and adenine and guanine both double ringed purines
c. basic building blocks for both RNA and DNA
5. basic structure of DNA
a. 2 strands of nucleotides joined together to form a twisted ladder like structure the double helix
b. Uprights of ladder are formed by covalent bonds between the deoxyribose molecules and the phosphate groups of adjacent nucleotides
c. Rungs are formed by the bases of the nucleotides of one upright connected to the bases of the other upright by hydrogen bonds
d. Each nucleotide of DNA contains one of the organic bases
i. Adenine
ii. Thymine
iii. Cytosine
iv. guanine
e. Adenine binds only to thymine because the structure of these organic bases allows 2 hydrogen bonds to form between them
f. Cytosine binds only to guanine because the structure of these organic bases allows 3 hydrogen bonds to form between them
g. The sequence of organic bases in DNA molecules stores genetic info and each DNA molecule consists of millions of organic bases, their sequence determines the type and sequence of amino acids in the protein molecules
h. Enzymes are proteins so DNA structure determines the rate and type of chemical reactions that occur in cells by controlling enzyme structure
i. The info in DNA ultimately defines all cellular activities
6. RNA structure
a. Similar to a single strand of DNA
b. 4 different nucleotides make up the RNA molecule and the organic bases are the same except that thymine is replaced with uracil
c. Uracil can bind only to adenine
Adenosine Triphospate ATP