Chapter 2 Chemical Organization

8/13/2019 Chapter 2 Chemical Organization

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The Chemical Level of

Organization

Chapter 2


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Ch 2 Outline

Atomic structure

Molecules/compounds

Chemical Rxns

Enzymes

Organic vs inorganic

Water properties

pH

Structure & function macromolecules


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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 differentcharacteristics

Chemical characteristics determine physiology at

the molecular and cellular levels


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Atoms Subatomic Particles

Proton Positive charge, 1 mass unit

Neutron

Neutral, 1 mass unit

Electron

Negative charge, low mass

Electrons

Neutrons

Protons

-Change the number of neutrons & electrons-

same characteristics, properties- same atom

-Change the number of protons- different atom!


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Atomic Structure

Atomic number Number of protons

Equal to number of electrons

Mass number Number of protons plus neutrons

Atomic Number

Atomic Mass

proton


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Atomic Structure

Nucleus *Contains protons and neutrons

Electron

Cloud*Contains electrons

traveling at high speed

Electrical Force-

negative charge on

electron attracted to

positively charged

protons


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Elements and Isotopes

Elements-pure substance composed of atoms ofonly 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


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Isotopes

Same element- different # of neutrons

Atomic number stay same

Atomic mass will differ

Carbonatomic number 6

Carbon 12- _6_ neutrons



All have 6 protons! # protons does not change!


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Electrons and Energy Levels

Electrons in the electron cloud determine thereactivityof 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


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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

A t f El t i t


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Arrangement of Electrons into

Energy Levels

Lowest energy shell

Fills first

Can hold two electrons

A t f El t i t


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Arrangement of Electrons into

Energy Levels

Electrons fill in order, 1stshell,

2ndshell, 3rdshell, etc. moving

away from nucleus.

2nd

shellholds 8

electrons

.


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Valence Shell

Number of electrons in valence shell determinesthe 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


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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 partialelectrical attractions

Ionic bonds: attraction between cations(electron

donor) and anions(electron acceptor)

Covalent bonds: strong electron bonds involving

shared electrons


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Chemical Bonds

Chemical bonds form molecules & compounds Molecules-2 or more atoms joined by strong

bonds

Compounds-2 or more atoms of DIFFERENT

ELEMENTSjoined by strong or weak bonds

Compounds are all molecules, but not all

molecules are compounds

H2= molecule only H2O = molecule and compound


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Ionic Bonds

One atom- electron donor-loses one or moreelectrons 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


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Formation of Ionic Bonds


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Formation of Ionic Bonds


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Covalent Bonds

Involve the sharing of pairs of electronsbetween 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)


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Covalent Bonds


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Covalent Bonds

Nonpolar covalent bonds- involve equalsharing 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 moleculeslike water

Polar Covalent Bonds and


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Polar Covalent Bonds and

Water Structure


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Hydrogen Bonds

Bonds between adjacent molecules, not atoms

Involve slightly positive and slightly negative

portions of polar molecules being attracted to

one another

Hydrogen bondsbetweenH2O molecules

cause surface tension

Hydrogen Bonds between Water


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Hydrogen Bonds between Water

Molecules

Hydrogen

Bond


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Chemical Reactions

Reactants- materials going into a reaction

Products- materials coming out of a reaction

Metabolism- all of the reactions that are occurringat one time

Growth, repair, maintenance, energy, secretion,

movement


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Basic Energy Concepts

Energy- capacity to do work Work- change in mass or distance, (movement

of an object or change in the physical structureof matter)

Kinetic energy- energy of motion

Potential energy- stored energy

Chemical energy- potential energy stored inchemical bonds


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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


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Chemical Reactions

Decomposition reaction(catabolism) Breaks chemical bonds

ABA + B

Hydrolysis: ABCDE + H2OABCH + HODE

Add water


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Chemical Reactions

Synthesis reaction(anabolism) Forms chemical bonds

A + BAB

Dehydrationsynthesis (condensation)

ABCH + HODEABCDE + H2O

Lose a water


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Chemical Reactions

Exchange reaction- involves decomposition first, thensynthesis

AB + CDAD + CB

Reversible reaction-rxn occurs simultaneously inboth directions

ABA + 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


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Enzymes

Chemical rxns in cells cannot start without help

Activation energy-amount of energy needed to

get a reaction started

Enzymes-protein catalyststhat loweractivation

energy of reactions

Enzyme 1

A B

Reaction 1

Enzyme 2

C

Reaction 2

Enzyme 3

D

Reaction 3

ProductStarting

molecule


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Effect of Enzymes on Activation Energy


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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


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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


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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


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Properties of Water

Solubility- ability to dissolve a solute in a solventto make a solution (aqueous)

Reactivity- most body chemistry occurs in water

Dehydration, hydrolysis rxns

High heat capacity- ability to absorb and retainheat

Takes a lot of heat liquid

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

Lubrication- to moisten and reduce friction

Knee caps, internal organs

Di i ti f i & l


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Ionization Dissociation of ions & polarcompounds in water

Polar water molecules formhydration spheres around

ions & small polar molecules

to keep them in solution.


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Electrolytes & Body Fluids

Electrolytes- inorganic ions that conduct

electricity in solution

Electrolyte imbalanceseriously disturbs vital

body functions


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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
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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


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pH and Homeostasis

Acidic:pH lower than 7.0

High H+concentration

Low OHconcentration

Basic(or alkaline): pH higher than 7.0 Low H+concentration

High OHconcentration

Acidic Basic

0 147H+> OH- 0H-> H+

[H+] = [OH-]

C


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pH and Hydrogen Ion Concentration

Inverse relationship: more H+ions mean

lowerpH, less H+ions mean higherpH

A id d B


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Acids and Bases

Acid-solute that adds hydrogen ions to a solution

Proton donor

Strong acids dissociate completely in solution

HCLH++ Cl-

Base-solute that removes hydrogen ions from a solution

Proton acceptor

Strong bases dissociate completely in solution NaOHNa++ OH-

W k A id /B & S lt


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Weak Acids/Bases & Salts

Weak acids and weak bases Fail to dissociate completely

Help to balance the pH

H2

CO3

H++ HCO3

-

Salts- solutes that dissociate into cations &anions other than hydrogen ions (H+) and

hydroxide ions (OH-)

B ff d H C t l


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Buffers and pH Control

Buffers-compounds that stabilize pH of asolution 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

O i M l l


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Organic Molecules

Contain H, C, and usually O

Covalently bonded

Contain functional groups that determine

chemistry

Carbohydrates

Lipids Proteins (amino acids)

Nucleic acids

I t t F ti l G


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Important Functional Groups

*Dont need to

memorize

structure but I

will refer tothese through

out the course

so just

familiarize

yourself with

them if you arenot already.

C b h d t


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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

P l h id


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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

St t f Gl


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Structure of Glycogen

Animal starch- glycogenMany side branches of

glucose molecules

Does not dissolved inwater or body fluids

Muscle cells make &

storeBreak it down when

need energy


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Li id


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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 Fatt Acids


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Lipids- Fatty Acids

Long chains of carbon & hydrogen with a

carboxylic acid group (COOH) at one end

Relatively nonpolar- exceptcarboxylic group

Fatty acids may be

Saturatedwith hydrogen (no covalent bonds)

Unsaturated(one or more double bonds): monounsaturated = one double bond

polyunsaturated = two or more double bonds

Fatty Acids


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Fatty Acids

.

Fatty Acids


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Fatty Acids

Lipids Eicosanoids


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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


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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


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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


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Steroids

Lipids Phospholipids & Glycolipids


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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


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Proteins


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Proteins

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

Basic building blocks- 20 amino acids

Peptide

bondSide chains

Backbone

7 Major Protein Functions


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7 Major Protein Functions

Support Structural proteins

Movement

Contractile proteins

Transport

Transport (carrier)

proteins

Buffering Regulation of pH

Metabolic regulation

Enzymes

Coordination &control

Hormones

DefenseAntibodies

Protein Structure


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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


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Formation of Peptide Bonds

*You should

know a

peptide bond

forms proteins

by joining

amino acids(dehydration

rxn)

Proteins


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Proteins

Fibrous proteins- structural sheets orstrands

Tough, durable, insoluble in water (structural role)

Globular proteins- soluble spheres withactive functions

Compact, soluble

Protein function is based on shape

Shape is based on sequence of amino acids

Globular & Fibrous Proteins


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Globular & Fibrous Proteins

Globular protein

Enzyme Function


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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


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Enzyme Structure & Function

Cofactors & Enzyme Function


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Cofactors & Enzyme Function

Cofactor- ion or molecule that binds to anenzyme before substrates can bind

Ca2+, Mg2+

Coenzyme- nonprotein organic cofactors

(vitamins)

Isozymes- two enzymes that can catalyze

the same reaction

Glycoproteins and Proteoglycans


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Glycoproteins and Proteoglycans

Glycoproteins- large protein + smallcarbohydrate

Enzymes, antibodies, hormones, receptors,

mucus production

Proteoglycans-large polysaccharides +

polypeptides

Promote viscosity in tissue fluids

Nucleic Acids


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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


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Structure of Nucleic Acids

DNA and RNA are strings of nucleotides

deoxyribose or ribose

A, G, T, C, or U

Nitrogenous Bases


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Nitrogenous Bases

PURINES

PYRIMIDINES

Nucleic Acids


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Nucleic Acids

DNA-double stranded, bases hydrogen bonds tohold double helix together

RNA-single strand

Complementary base pairs: purines pair withpyrimidines

DNA: adenine (A) & thymine (T)

cytosine (C) & guanine (G)

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


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Structureof

Nucleic

Acids

Types of RNA


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Types of RNA

Messenger RNA (mRNA)-transcript of DNA

Transfer RNA (tRNA)-

transfers amino acids toribosome

Ribosomal RNA (rRNA)-

forms ribosome whichholds mRNA in place and

aligns tRNA, catalyzing

protein formation

Ribosome

mRNA

tRNA

ATP


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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 ofa high-energy phosphate group to a molecule)


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ATP

Chapter 2 Chemical Organization

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