chapter 2: the chemical level of organization copyright 2009, john wiley & sons, inc

Chapter 2: The Chemical

Level of Organization

Copyright 2009, John Wiley & Sons, Inc.

Biology based on principles of chemistry and physics

Living organisms are collection of atoms and molecules

Life’s processes dependent on Chemistry

All life composed of Matter (Anything that has mass and

occupies space)

Why Chemistry?

Matter consists of chemical elements in pure form and in combinations called compounds

• Organisms are composed of matter• Matter is anything that takes up space and has mass

• Since chemicals compose your body and all body activities are chemical in nature, it is important to become familiar with the language and fundamental concepts of chemistry.

• We are taking the approach that in order to understand living systems you have to understand what they are made of.

How Matter is Organized

Chemical Elements All forms of matter are composed of chemical

elements which are substances that cannot be split into simpler substances by ordinary chemical means.

Elements are given letter abbreviations called chemical symbols.

Trace elements are present in tiny amounts


Periodic Table of the Elements

Structure of Atoms

Units of matter of all chemical elements are called atoms. An element is a quantity of matter composed of atoms of the same type.

Atoms contain: Nucleus: protons (p+) & neutrons (neutral

charge) Electrons (e-) surround the nucleus as a

cloud (electron shells are designated regions of the cloud)


2 Representations of Atomic Structure

Atomic Number and Mass Number Atomic number is number of protons in the

nucleus. Mass number is the sum of its protons and

neutrons.


Atomic Mass

Mass is measured as a dalton (atomic mass unit)

Neutron has mass of 1.008 daltons proton has mass of 1.007 daltons electron has mass of 0.0005 dalton

Atomic mass (atomic weight) is close to the mass number of its most abundant isotope.


Atomic Number and Mass Number Atomic Mass

The atomic mass, also called the atomic weight, of an element is the average mass of all its naturally occurring isotopes and reflects the relative abundance of isotopes with different mass numbers.

The mass of a single atom is slightly less than the sum of the masses of its neutrons, protons, and electrons because some mass (less than1%) was lost when the atom’s components came together to form an atom.


Ions, Molecules, Compounds, Free Radicals Ions - an atom that gave up or gained an electron

written with its chemical symbol and (+) or (-) Molecule - atoms share electrons (2 or more similar elements)

written as molecular formula showing the number of atoms of each element

■ Compound – 2 or more different elements

□ has characteristics different from those of its elements Free Radical - an electrically charged atom or group of atoms with

an unpaired electron in its outermost shell Unstable and highly reactive; can become stable by giving up an electron taking an electron from another molecule Antioxidants are substances that inactivate oxygen-derived free

radicals


Chemical Bonds The atoms of a molecule are held together by forces of

attraction called chemical bonds (union between electron structures of atoms)

The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the valence shell.

Electrons:

-Carry a negative charge

-Repel one another but attracted to protons in the nucleus

- It takes energy to hold electrons in place

-Move in orbitals - volumes of space that surround the nucleus


Electrons and Electron Shells

Only outer shell electrons can interact (form bonds)! If outermost shell is full, element is stable (He) If outermost shell is not full, unstable and can

bond The 1st shell can hold 2 electrons The 2nd shell can hold 8 electrons Stability is goal : by gaining, losing or sharing

electrons

Ionic Bonds When an atom loses or gains a valence electron, ions

are formed Charge difference attracts the two ions to each other

Positively and negatively charged ions are attracted to one another.

Cations are positively charged ions that have given up one or more electrons (they are electron donors).

Anions are negatively charged ions that have picked up one or more electrons that another atom has lost (they are electron acceptors).


The Ionic Bond Formation

Covalent Bonds Covalent bonds are formed by the atoms of molecules sharing one,

two, or three pairs of their valence electrons. Covalent bonds are the most common and strongest chemical

bonds in the body. Single, double, or triple covalent bonds are formed by sharing

one, two, or three pairs of electrons, respectively. Covalent bonds may be nonpolar or polar.

Nonpolar covalent bond -atoms share the electrons equally; one atom does not attract the shared electrons more strongly than the other atom

Polar covalent bond- unequal sharing of electrons between atoms. In a water molecule, Oxygen has greater electronegativity & attracts the hydrogen electrons more strongly;



Polar Covalent Bond

Nonpolar Covalent Bond

fd

TEST YOURSELF!!

How many covalent bonds can each of these atoms form??

Hydrogen Bonds An attraction between a

slightly positive hydrogen atom in one molecule and a slightly negative atom (usually oxygen) in another molecule

weak intermolecular bonds; serve as links between molecules.

help determine three-dimensional shape

give water considerable cohesion which creates a very high surface tension


Chemical Reactions (Metabolism) When new bonds form or old bonds are broken

Metabolism is all the chemical reactions in the body Law of conservation of mass = total mass of reactants equals the total mass of the

products Require a source of energy and a catalyst (enzymes) Occur in liquid environment – water Influenced by: Temperature ; Concentration of reactants; Catalysts

Energy and Chemical Reactions Chemical reactions involve energy changes

Two principal classes of energy: potential energy = stored energy kinetic energy = energy of motion

Chemical energy is potential energy stored in the bond of molecules digestion of food releases that chemical energy so that it

can be converted to heat or mechanical energy Law of conservation of energy

energy can neither be created nor destroyed--just converted from one form to another

2-25

• Five Types of Energy

1. Mechanical - resulting from the position & movement of objects Ex. Moving a limb

2. Chemical – energy within chemical bonds Ex. ATP + H2O ADP + H2PO4 + E+

3. Heat - flows between objects that are different temperatures Ex. Human body’s chemical rxns release heat as a by-product

and this helps to maintain body temperature

4. Electric - ability of an electric current to produce work, heat, light, or other forms of energy. It is measured in kilowatthours.

5. Electromagnetic - reflected or emitted from objects in the form of electrical and magnetic waves that can travel through space

26

Energy Transfer in Chemical Reactions Forming new bonds releases energy & breaking old

bonds requires energy Chemical reactions usually involve both

exergonic reactions release more energy endergonic reactions absorb more energy than they

release Human metabolism couples exergonic and endergonic

reactions, so that the energy released from one reaction will drive the other. Glucose breakdown releases energy used to build

ATP molecules that store that energy for later use in other reactions

Activation Energy Atoms, ions & molecules are continuously moving & collidingActivation energy is the collision energy needed to break bonds & begin a reaction


Factors that Cause a Collision and Chemical Reaction Concentration

Temperature Catalysts are chemical compounds that speed up chemical reactions

by lowering the activation energy needed for a reaction to occur. A catalyst does not alter the difference in potential energy between

the reactants and products. It only lowers the amount of energy needed to get the reaction started. A catalyst helps to properly orient the colliding particles of matter

so that a reaction can occur at a lower collision speed. The catalyst itself is unchanged at the end of the reaction; it is

often re-used many times.


Catalysts and chemical reactions


Types of Chemical Reactions

Synthesis Reactions--Anabolism -Two or more atoms, ions or molecules combine to form new

& larger molecules

-Anabolism - all the synthesis reactions in the body

-Usually endergonic→absorb more energy than they release

-Example combining amino acids → protein molecule

Decomposition Reactions—Catabolism-Large molecules are split into smaller atoms, ions or molecules

-Catabolism -all decomposition reactions in the body

-Usually are exergonic→release more energy than they absorb

Types of Chemical Reactions

Exchange Reactions Substances exchange atoms

consist of both synthesis and decomposition reactions Example: HCl + NaHCO3 → H2CO3 + NaCl

ions have been exchanged between substances

Reversible ReactionsReactants can become products or products can revert to the

original reactants

Indicated by the 2 arrows pointing in opposite directions between the reactants and the products

AB ↔ A + B

Oxidation-Reduction Reactions Oxidation is the loss of electrons from a molecule (decreases

its potential energy); acceptor of the electron is often oxygen Reduction is the gain of electrons by a molecule

increases its potential energy In the body, oxidation-reduction reactions are coupled & occur

simultaneously

Inorganic Compounds & Solvents Most of the chemicals in the body are

compounds Inorganic compounds

usually lack carbon & are structurally simple Exceptions: CO , CO2 , HCO3 Water, Oxygen, CO2, Salts, Acids & Bases

Organic compounds contain carbon & usually hydrogen always have covalent bonds

Water – most abundant & importantinorganic compound in living systems

Characteristics of H2O

1. Polar molecule:– b/c it is polar it forms H+ bonds

with other H2O molecules forming a lattice structure w/in the H2O

2. % of body’s weight– 50% in ♀ (> body fat than ♂)– 60% in ♂

3. % of blood plasma– 92% H2O

AP1: Ch. 2: Chemical Basis of Life 37

Polar Water Molecules


H2O: Functions in living organisms1. Stabilizing Body Temp.

– H2O has a high specific heat (meaning it takes a large amount of e+ to raise its temperature)

– Thus it is resistant to temperature ’s

– H2O also evaporates (thus it can be sweat used to cool the body when it evaporates and takes the “heat” with it)

2. Protection– Acts as a lubricant to

prevent damage from friction

– It also forms a “fluid cushion” around the organs (ex. CSF)

3. Chemical Rxns– Reacting molecules must be

dissolved in H2O for many of the bodies chemical rxns

– **Hydrolysis– **Dehydration Synthesis

4. Mixing Medium– Mixture: combination of 2 or

more substances blended together but not chemically combined

a. Solutionb. Suspensionc. Colloid

39

3 Common MixturesA mixture is a combination of elements or compounds that are

physically blended together but are not bound by chemical bonds.

Solution: a substance called the solvent dissolves another substance called the solute. Usually there is more solvent than solute in a solution.

A colloid differs from a solution mainly on the basis of the size of its particles with the particles in the colloid being large enough to scatter light.

Suspension: the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out.


Concentration

The concentration of a molecule is a way of stating the amount of that molecule dissolved in solution.

Percent gives the relative mass of a solute found in a given volume of solution.

A mole is the name for the number of atoms in an atomic weight of that element, or the number of molecules in a molecular weight of that type of molecule, with the molecular weight being the sum of all the atomic weights of the atoms that make up the molecule.


Acids & BasesAcid

A proton (H+) donor

Base

A proton (H+) acceptor OH- is what is usually found in

solution that will bind to free H+’s

42

Strong Acid/Base

• Either will completely dissociate when put into H2O, releasing all of the H+ or OH- in their make-up

• The rxn is not freely reversable

• Ex.• HCl H+ + Cl-

• NaOH Na+ + OH-

Weak Acid/Base

• A proton (H+) acceptor• OH- is what is usually

found in solution that will bind to free H+’s

• Rxn is reversible• Ex.

• H3COOH ↔ CH3COO- + H+

Dissociation of Acids, Bases, and Salts


pHpH scale expresses hydrogen ion (H+) concentration in a solution.

scale range = 0-14

neutral = 7

Acids release H+

thus increasing [H+]

pH values < 7

Bases lower [H+]

bond up H+ or

Release OH-

pH values > 7

Why do we care about pH?

pH can affect:

Shapes and functions of molecules

Rates of many chemical reactions

Ability of two molecules to bind to each other

Ability of ions or molecules to dissolve in water

Organisms usually tolerate only small changes in pH

BLOOD pH MUST BE MAINTAINED AT 7.35-7.45

Buffers help to keep a relatively constant pH

Buffers act as a reservoir for hydrogen ions, donating or removing

them from solution as necessary.

Buffers- convert strong acids or bases→ weak acids or bases

Examples of buffers used by living systems include: Bicarbonate, Phosphates, Amino Acids, Proteins as Components

H2CO3 ↔ H+ + HCO3-

Carbonic Acid Proton Bicarbonate Ion Conjugate Acid (H+ donor) Conjugate Base (H+ acceptor)

b/c the rxn is reversible: In a [H+] flow in In a [H+] flow in Thus: H2CO3 and HCO3

- remain in constant equilibrium

The greater the buffer concentration the more resistant to , but pH may still just not as drastically as seen w/o the buffer


Oxygen

21% of earth’s atmosphere is O2

Essential to lives of most animals

Humans use it in the final step in a series of rxns in which e+ is extracted from food molecules

Carbon Dioxide

Byproduct of organic molecule metabolism

A small % is eliminated via exhalation

Accumulation of high amounts is toxic to cells


• Carbon is unique in that it can form covalent bonds w/ up to 4 other atoms allowing the formation of the large, diverse, complicated molecules required for life.

• These molecules are:1. Carbohydrates2. Lipids3. Proteins4. Nucleic Acids

• Carbon Backbone: series of C atoms bound together by covalent bonds

• CB allows for variation in length as well as highly varied combinations of atoms.


Carbohydrates Made up of C, H, O in a 1:2:1 ratio Glucose : C6-H12-O6• Carbo: Atom Hydrates: Hydrated

• Range from small to large in size1. Monosaccharide- Mono 1 Simple Sugar

2. Disaccharide- Di 2

3. Polysaccharide- Complex Sugar

• Functions:

A. Structural: ribose and deoxyribose (DNA, RNA, ATP)

B. Energy: simple sugars(monosaccharides) can be used as an immediate e+ source, complex sugars must be processed before use

• Glycogen (polysaccharide) - e+ storage molecule

C. Bulk: cellulose (polysaccharide) forms the bulk of feces


Monosaccharides = 1 (mono) sugar


Disaccharides Combining 2 monosaccharides by dehydration

synthesis releases a water molecule. sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)


Polysaccharides (PS) = many (poly) sugars

• Many MS’s bound together to form long chains (can be straight or branched)

• 3 major types:– In animals you find 1 type in plants 2 types

a) Glycogen: “animal starch”; used as an e+ storage molecule. When quickly metabolized it results in e+ for cells

b) Starch: long chains of glucose used for e+ storage in plants

• Humans can break it down & use it for e+

c) Cellulose• Long chains of glucose that fxn as a structural

molecule in plants• Humans can’t break it down & use it for e+,

thus it b/comes bulk of feces

53

Lipids (a.k.a. fats)• Major components: C, H, & O • Minor components: P & N• Compared to carb’s, lipids do not have 2:1 ratio of H

to O and have a lower ratio of O to C, this makes them less polar thus they can be dissolved in non-polar organic solvents (acetone, alcohol)

• 4 major groups:– Triglycerides– Phospholipids– Steroids– “Other”


• Fxns of lipids:A. Protection: surrounds and protects organsB. Insulation: fat under the skin prevents heat loss; myelin

sheaths electrically insulate axons of neuronsC. Regulation: steroids regulates physiological

processes prostaglandins regulate inflammationD. Vitamins: “fat soluble” vitamins do many things

• Vit A forms retinol req’d for night vision• Vit D Promotes Ca2+ uptake in bone tissue• Vit E Promotes healing• Vit K necessary to form clotting factors

E. Energy: can be broken down to yield more e+ than either carb’s or proteins


• Make-up 95% of fats in the human body

• 1- glycerol + 3 Fatty Acids (FA’s)• FA’s differ from each other by #

of C’s and degree of saturation– 2 types:

1. Saturated• Only single covalent bond btwn

C’s in the carbon backbone

2. Unsaturated• 1 or more double covalent bond

btwn C’s in the carbon backbonea) Monounsaturated

b) Polyunsaturated


Gly

cero

l

Fatty Acid

Fatty Acid

Fatty Acid

Triglycerides

Triglycerides


Phospholipids (PL) Glycerol + 2 FA’s + phosphate

containing molecule Notice structurally similar to TG’s

Polar Molecule: Hydrophilic Head (Polar) Hydrophobic Tails (Non-polar)

Essential in the cell membrane’s structure


Chemical Nature of Phospholipids

2-59

head tails

Steroids

• Structurally they are a unique lipid, but their solubility characteristics are similar

• All composed of C’s bound together in a 4-ring-like structure

• Important Examples:– Cholesterol (building blocks for

other steroids)Ingest too much heart disease, but it is still essential to diet

– Bile Salts– Estrogen– Progesterone– Testosterone


• Eicosanoids– Group of important

molecules derived from FA’s

– Made in most cells – Important regulatory

molecules– Examples:a) Prostaglandins: implicated

in regulation of hormones for blood clotting, some reproductive fxns, and more (*Asprin*

b) Thromboxanesc) Leukotrienes

• Fat Soluble Vitamins– Structurally not similar to

one another but they are non-polar molecules essential to normal body fxn


Other Lipids

Proteins

Major components: C, H, O, & N Minor components: S, P, Fe, and I Protein’s molecular mass can be huge:

NaCl= 58 Glucose= 108 Proteins 1000 to several million


Fxns of proteins1. Regulation

– Enz’s control chem rxns and hormones regulate many physiological processes

2. Transport– Can help to transport things in the watery environment of the

blood & can control mvmt in & out of cell3. Protection

– Antibodies and complement system proteins protect against foreign invaders

4. Contraction– Actin and Myosin and proteins involved in muscle movement

5. Structure– Collagen fibers give structural framework– Keratin lends strength to hair, skin, nails

6. Energy– Can be broken down to produce e+ equals the same yield as

carb’s63

Protein Structure

The building blocks of proteins are amino acids(AA): These are made up of a central C with

an Amine group at one end and a carboxyl group at the other

The R-Group varies from AA to AA Btwn each AA the Amine and Carboxyl

groups bind to each other and form Peptide Bonds. Thus the reason proteins are often referred to as polypeptides.

64

All

20

Am

ino A

cid

S

tru

ctu

res


Formation of a Dipeptide Bond Dipeptides formed from 2 amino acids joined by a

covalent bond called a peptide bond dehydration synthesis

Polypeptides chains contain 10 to 2000 amino acids.


4 Levels Protein Structure

1. Primary (1o)- Sequence of aa bound by peptide bonds

2. Secondary (2o) a-helix & b-pleated sheet

- Local structure that results from H-bonding

-If these bonds are broken by temperature

or pH the protein will unfold & become

non-functional

3. Tertiary (3o)- 3D structure-Caused by the interactions btwn the polypeptide and its immediate environment

4. Quaternary (4o)-Spatial relationships between individual subunits


Proteins : Enzymes• Protein catalyst that increases the

rate of chemical rxn w/o being ed itself

• An enz’s 3-d shape is essential for its fxn

• Lock & Key Model (old name)– Lock: Active Site– Key: Reactants

• Induced fit model (new name)– more correct term– The enz can shape significantly to fit

reactants• Enz’s lower activation e+ b/c they

orient the reactant in such a way that chem rxn is more likely to occur

69

Enzyme binds reactants Combines reactants Releases reactant so that it can do it

all over again It is capable of catalyzing multiple

reactions Some enz’s require co-factors to fxn

or an organic molecule Co-factors: ions

Usually finalize the shape of the active site

Organic Molecule: co-enzymes

-ase …this suffix means enzyme

70

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex

Enzyme

SucraseActive siteof enzyme

Substrates

Sucrose andWater

H2O

Mechanism of enzyme action

1

Enzyme catalyzesreaction and transformssubstrate into products

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose

Fructose

Enzyme


Substrates

Sucrose andWater

Products

H2O


1

2When reaction is complete,enzyme is unchanged andfree to catalyze same reactionagain on a new substrate

Enzyme catalyzesreaction and transformssubstrate into products

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose

Fructose

Enzyme


Substrates

Sucrose andWater

Products

H2O


1

3 2

Nucleic Acids - Made-up of C,H,O,N & P

DNA- genetic code

Deoxyribonucleic Acid

Double Helix

RNA- mRNA, rRNA, tRNA

Ribonucleic Acid

Single stranded

•building blocks are called nucleotides

PhosphateGroup

Pentose Sugar

NitrogenousBase

Basic Nucleotide →

Nitrogenous Organic Bases- 2 types Purines

Guanine Adenine

Pyrimidines Cytosine Thymine Uracil

AP1

DNA bases• Adenine• Guanine• Cytosine• Thymine

RNA bases• Uracil• Guanine• Cytosine• Adenine

RNA (single stranded) DNA (Double Stranded)

AP1

DNA• DNA is a double helix

– “twisted ladder”• Vertically nucleotides are held together

via a covalent bond between the

phosphate group of 1 NA and the next• Horizontally, nucleotides are held

together via a H bond between

nitrogenous bases next to each other*NB’s must have to correct partner to bind to**

→ complementary base pairing

– DNA :T=A G=C – RNA: U=A G=C

DNA• The two opposing strands of DNA

also run antiparallel to each other.– Meaning the sugar phosphate

backbone of 1 strand runs the opposite direction of it’s partner• 5’ 3’• 3’ 5’

• Within DNA the sequence of bases is a “code” that stores information used to determine the structure and fxn of cells

• Gene: sequence of DNA that directs the synthesis of an RNA molecule that will become a protein

Adenosine Triphosphate (ATP)

Temporarymolecular storage ofenergy as it is beingtransferred fromexergonic catabolicreactions to cellularactivities


Formation & Usage of ATP Hydrolysis of ATP (removal of terminal phosphate group by

enzyme -- ATPase) releases energy leaves ADP (adenosine diphosphate)

Synthesis of ATP enzyme ATP synthase catalyzes the addition of the

terminal phosphate group to ADP energy from 1 glucose molecule is used during both

anaerobic and aerobic respiration to create 36 to 38 molecules of ATP

Cyanide Poisoning: The way cyanide works is by impeding the production of

ATP within the mitochondria


chapter 2: the chemical level of organization copyright 2009, john wiley & sons, inc

Documents

john wiley sons

mass numberatomic number

average mass

number of atoms

different mass numbers

dalton atomic mass unitneutron

number of protons

different elements