The Chemical Level of Organization

Chapter 2

Ch 2 Outline
Atomic structure Molecules/compounds Chemical Rxns Enzymes Organic vs inorganic Water properties pH Structure & function macromolecules

Atoms
Matter- anything that takes up space & has mass
Made up of atoms- smallest stable units of matter

Atoms join together to form chemicals with different characteristics Chemical characteristics determine physiology at the molecular and cellular levels

Atoms Subatomic Particles

Proton
Positive charge, 1 mass unit
Electrons

Neutron
Neutral, 1 mass unit
Protons Neutrons

Electron
Negative charge, low mass
-Change the number of neutrons & electronssame characteristics, properties- same atom -Change the number of protons- different atom!

Atomic Structure
Atomic number
Number of protons Equal to number of electrons

Mass number
Number of protons plus neutrons

proton

Atomic Number

Atomic Mass

Atomic Structure
Nucleus
*Contains protons and neutrons

Electron Cloud

*Contains electrons traveling at high speed

Electrical Forcenegative charge on electron attracted to positively charged protons

Elements and Isotopes

Elements- pure substance composed of atoms of only 1 kind, uniform composition & properties
Determined by atomic number of atom (protons) Cannot be broken down or changed

Isotopes- specific version of an element based on its mass number

Same element, different number of neutrons Only neutrons are different because the number of protons determines the element

Isotopes
Same element- different # of neutrons
Atomic number stay same Atomic mass will differ

Carbon atomic number 6

Carbon 12- _6_ neutrons Carbon 13- _7_ neutrons Carbon 14- _8_ neutrons

All have 6 protons! # protons does not change!

Electrons and Energy Levels

Electrons in the electron cloud determine the reactivity of an atom

Electron cloud contains shells- energy levels that hold a maximum number of electrons
Lower shells fill 1st- closest to nucleus Outermost shell- valence shell, determines bonding

 Energy level- state of potential energy electrons possess

Correlates to average distance from nucleus Electron shells
Shell 1- closest to nucleus, lowest potential energy Shell 2- increased energy and so forth

Arrangement of Electrons into Energy Levels

Lowest energy shell Fills first Can hold two electrons

Arrangement of Electrons into Energy Levels

2nd shell holds 8 electrons .

Electrons fill in order, 1st shell, 2nd shell, 3rd shell, etc. moving away from nucleus.

Valence Shell
Number of electrons in valence shell determines the chemical properties of the element Atom with unfilled valence shell- unstable
They will react with other atoms to fill their shells!

Atoms with full valence- stable & unreactive

Hydrogen

Helium

Chemical Bonds
Chemical bonds involve the sharing, gaining, and losing of electrons in the valence shell
Three majors types of chemical bonds
Hydrogen bonds: weak polar bonds based on partial electrical attractions
Ionic bonds: attraction between cations (electron donor) and anions (electron acceptor) Covalent bonds: strong electron bonds involving shared electrons

Chemical Bonds
Chemical bonds form molecules & compounds
Molecules- 2 or more atoms joined by strong bonds Compounds- 2 or more atoms of DIFFERENT ELEMENTS joined by strong or weak bonds

Compounds are all molecules, but not all molecules are compounds
H2 = molecule only H2O = molecule and compound

Ionic Bonds
One atom- electron donor -loses one or more electrons and becomes a cation, (positive charge) Another atom- electron acceptor -gains those same electrons, becomes an anion, (negative charge) Attraction between the opposite charges then draws the two ions together

Formation of Ionic Bonds

Formation of Ionic Bonds

Covalent Bonds
Involve the sharing of pairs of electrons between atoms
One electron is donated by each atom to make the pair of electrons
Sharing one pair of electrons is a single covalent bond (strong bond) Sharing two pairs of electrons is a double covalent bond (stronger bond) Sharing three pairs of electrons is a triple covalent bond (strongest bond)

Covalent Bonds

Covalent Bonds
Nonpolar covalent bonds- involve equal sharing of electrons
Atoms involved in the bond have equal pull for the electrons

Polar covalent bonds- involve unequal sharing of electrons

One of atoms involved in the bond has a disproportionately strong pull on the electrons Form polar molecules like water

Polar Covalent Bonds and Water Structure

Hydrogen Bonds
Bonds between adjacent molecules, not atoms Involve slightly positive and slightly negative portions of polar molecules being attracted to one another Hydrogen bonds between H2O molecules cause surface tension

Hydrogen Bonds between Water Molecules

Hydrogen Bond

Chemical Reactions
Reactants- materials going into a reaction Products- materials coming out of a reaction

Metabolism- all of the reactions that are occurring

at one time

Growth, repair, maintenance, energy, secretion, movement

Basic Energy Concepts

Energy- capacity to do work

Work- change in mass or distance, (movement of an object or change in the physical structure of matter)
Kinetic energy- energy of motion Potential energy- stored energy Chemical energy- potential energy stored in chemical bonds

Energy
Cannot be created or destroyed, only converted Conversion between kinetic and potential energy never 100% efficient
Some energy is always lost as heat Heat- increase in random molecular motion

Chemical Reactions
Decomposition reaction (catabolism)
Breaks chemical bonds AB A + B Hydrolysis: ABCDE + H2O ABCH + HODE

Add water

Chemical Reactions
Synthesis reaction (anabolism)
Forms chemical bonds A + B AB Dehydration synthesis (condensation) ABCH + HODE ABCDE + H2O

Lose a water

Chemical Reactions
Exchange reaction- involves decomposition first, then
synthesis AB + CD AD + CB

Reversible reaction -rxn occurs simultaneously in

both directions AB A + B At equilibrium amounts of chemicals do not change even though rxns are still occurring:
Seek equilibrium, balancing opposing reaction rates Add or remove reactants- rxn rates adjust to reach a new equilibrium

Enzymes
Chemical rxns in cells cannot start without help Activation energy- amount of energy needed to get a reaction started Enzymes- protein catalysts that lower activation energy of reactions
Enzyme 1 A Reaction 1 Starting molecule B Reaction 2 Enzyme 2 C Reaction 3 Product Enzyme 3 D

Effect of Enzymes on Activation Energy

Enzymes
Exergonic (exothermic) reactions
Produce more energy than they use
Give off energy

Endergonic (endothermic) reactions

Use more energy than they produce
Require energy to begin

Inorganic Vs Organic Compounds

Nutrients -essential molecules obtained from food Metabolites -molecules made or broken down in the body Inorganic -molecules not based on carbon and hydrogen
Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts

Organic -molecules based on carbon and hydrogen

Carbohydrates, proteins, lipids, nucleic acids

Importance of Water
Water accounts for up to 2/3 of your total body weight A solution is a uniform mixture of 2 or more substances Solute- atoms, ions, or molecules Solvent- medium, in which solutes are individually dispersed

Hydrogen bonding between water molecules accounts for unique properties

Properties of Water
Solubility- ability to dissolve a solute in a solvent
to make a solution (aqueous)

Reactivity- most body chemistry occurs in water

Dehydration, hydrolysis rxns

High heat capacity- ability to absorb and retain

heat
Takes a lot of heat liquid gas, carries great deal of heat (cooling effect), takes a lot of heat to change temp

Lubrication- to moisten and reduce friction

Knee caps, internal organs

Ionization

Dissociation of ions & polar compounds in water

Polar water molecules form hydration spheres around ions & small polar molecules to keep them in solution.

Electrolytes & Body Fluids

Electrolytes- inorganic ions that conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions

Hydrophilic & Hydrophobic Compounds

Hydrophilic
hydro- = water, philos = loving
interacts with water includes ions and polar molecules

Hydrophobic
phobos = fear

does NOT interact with water

includes nonpolar molecules, fats, and oils

pH and Homeostasis
pH- concentration of hydrogen ions (H+) in a solution
pH = -log [H+]

Neutral pH: [H+] = [OH-]

A balance of H+ and OH Pure water = 7.0

pH of human blood
Ranges from 7.35 to 7.45

pH and Homeostasis
Acidic: pH lower than 7.0
High H+ concentration Low OH concentration

Basic (or alkaline): pH higher than 7.0

Low H+ concentration High OH concentration Acidic
H+ > OH-

Basic
0H- > H+

7
[H+] = [OH-]

14

pH and Hydrogen Ion Concentration

Inverse relationship: more H+ ions mean lower pH, less H+ ions mean higher pH

Acids and Bases

Acid- solute that adds hydrogen ions to a solution
Proton donor Strong acids dissociate completely in solution HCL H+ + Cl-

Base- solute that removes hydrogen ions from a solution

Proton acceptor Strong bases dissociate completely in solution NaOH Na+ + OH-

Weak Acids/Bases & Salts

Weak acids and weak bases
Fail to dissociate completely Help to balance the pH H2CO3 H+ + HCO3-

Salts- solutes that dissociate into cations &

anions other than hydrogen ions (H+) and hydroxide ions (OH-)

Buffers and pH Control

Buffers- compounds that stabilize pH of a
solution by removing/replacing H+
Weak acid & its related salt compounds Neutralizes either strong acid or strong base Sodium bicarbonate is very important in humans

Antacids- basic compound that neutralizes

acid and forms a salt

Organic Molecules
Contain H, C, and usually O

Covalently bonded
Contain functional groups that determine chemistry
Carbohydrates Lipids

Proteins (amino acids)

Nucleic acids

Important Functional Groups

*Dont need to memorize structure but I will refer to these through out the course so just familiarize yourself with them if you are not already.

Carbohydrates
Contain C, H, O in 1:2:1 ratio Monosaccharides
Simple sugars with 3 to 7 carbon atoms Glucose, fructose, galactose

Disaccharides
Two simple sugars condensed by dehydration synthesis Sucrose, maltose

Polysaccharides
Many monosaccharides condensed by dehydration synthesis Glycogen, starch, cellulose

Polysaccharides
Large molecules of complex carbohydrates Straight, highly branched Structure or energy storage
Cellulose- structural component in plants
We cannot digest- fiber!

Starches- storage molecules

Potatoes, grains- main energy source

Structure of Glycogen
Animal starch- glycogen
Many side branches of glucose molecules

Does not dissolved in water or body fluids Muscle cells make & store
Break it down when need energy

Lipids
Hydrophobic molecules- fats, oils, waxes Made mostly of carbon and hydrogen atoms Make up cell membranes, important energy source

Include
Fatty acids Eicosanoids

Glycerides
Steroids Phospholipids and glycolipids

Lipids- Fatty Acids

Long chains of carbon & hydrogen with a carboxylic acid group (COOH) at one end Relatively nonpolar- except carboxylic group

Fatty acids may be Saturated with hydrogen (no covalent bonds) Unsaturated (one or more double bonds):
monounsaturated = one double bond polyunsaturated = two or more double bonds

Fatty Acids

Fatty Acids

Lipids- Eicosanoids
Derived from the fatty acid- arachidonic acid
Leukotrienes- active in immune system (injury & disease) Prostaglandins- local hormones, short-chain fatty acids
Pain, tissue damage, trigger labor contractions

Lipids- Glycerides
Fatty acids attached to a glycerol molecule Triglycerides- three fatty-acid tails
Also called triacylglycerols or neutral fats
Three important functions:
energy source
insulation protection

Lipids- Steroids
4 rings of C & H with functional groups Types of steroids:
Cholesterol:
Component of cell membranes, cell growth & division

Estrogens & testosterone:

Sex hormones- regulate sexual function

Corticosteroids & calcitriol:

Metabolic regulation, mineral balance

Bile salts:
Derived from steroids, process dietary fats

Steroids

Lipids- Phospholipids & Glycolipids

Our bodies can make both from fatty acids Diglycerides attached to either a phosphate group (phospholipid) or a sugar (glycolipid) Generally, both have hydrophilic heads & hydrophobic tails and are structural lipids, components of cell membranes

Phospholipids

Glycolipids

Proteins
Most abundant organic molecules Contain basic elements: C, H, O, N

Basic building blocks- 20 amino acids

Side chains Peptide bond

Backbone

7 Major Protein Functions

Support
Structural proteins

Buffering
Regulation of pH

Movement
Contractile proteins

Metabolic regulation
Enzymes

Transport
Transport (carrier) proteins

Coordination & control

Hormones

Defense
Antibodies

Protein Structure
Long chains of amino acids Amino acid structure
Central carbon atom Hydrogen atom Amino group
(NH2)

Carboxylic acid group

(COOH)

Variable side chain

R group

Formation of Peptide Bonds

*You should know a peptide bond forms proteins by joining amino acids (dehydration rxn)

Proteins
Fibrous proteins- structural sheets or strands
Tough, durable, insoluble in water (structural role)

Globular proteins- soluble spheres with active functions

Compact, soluble

Protein function is based on shape Shape is based on sequence of amino acids

Globular & Fibrous Proteins

Globular protein

Enzyme Function
Enzymes are catalysts
Proteins that lower the activation energy of a chemical reaction Are not changed or used up in the reaction Enzymes are also
Specific- will only work on limited types of substrates Limited- by their saturation Regulated- by other cellular chemicals

Enzyme Structure & Function

Cofactors & Enzyme Function

Cofactor- ion or molecule that binds to an enzyme before substrates can bind
Ca2+, Mg2+

Coenzyme- nonprotein organic cofactors (vitamins)

Isozymes- two enzymes that can catalyze the same reaction

Glycoproteins and Proteoglycans

Glycoproteins- large protein + small carbohydrate
Enzymes, antibodies, hormones, receptors, mucus production

Proteoglycans- large polysaccharides + polypeptides

Promote viscosity in tissue fluids

Nucleic Acids
Large organic molecules which store and process information at the molecular level Deoxyribonucleic Acid (DNA)
Determines inherited characteristics Directs protein synthesis Controls enzyme production Controls metabolism

Ribonucleic Acid (RNA)

Controls intermediate steps in protein synthesis

Structure of Nucleic Acids

DNA and RNA are strings of nucleotides

deoxyribose or ribose

A, G, T, C, or U

Nitrogenous Bases
PURINES PYRIMIDINES

Nucleic Acids
DNA- double stranded, bases hydrogen bonds to hold double helix together

RNA- single strand

Complementary base pairs: purines pair with pyrimidines DNA:
adenine (A) & thymine (T) cytosine (C) & guanine (G)

RNA:
uracil (U) replaces thymine (T), A & U

Structure of Nucleic Acids

Types of RNA
Messenger RNA (mRNA)transcript of DNA

Transfer RNA (tRNA)transfers amino acids to ribosome

Ribosomal RNA (rRNA)forms ribosome which holds mRNA in place and aligns tRNA, catalyzing protein formation

Ribosome

tRNA

mRNA

ATP
Nucleotides can be used to store energy
Adenosine diphosphate (ADP)
Two phosphate groups; di- = 2

Adenosine triphosphate (ATP)

Three phosphate groups; tri- = 3

ATPase- enzyme catalyzes phosphorylation (addition of

a high-energy phosphate group to a molecule)

ATP