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Chapter 2:

Chemistry

Comes Alive

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Why Chemistry???

• Chemistry is everywhere, especially

within the human body

• Chemistry drives biological processes

• We are composed of chemicals (water,

protein, fat, DNA, etc) and the

substances we ingest are chemicals as

well

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Structural Organization:

Chemical Level

• Atoms/ Elements

• Molecules/

Compounds

• Macromolecules 3

Basic Chemistry: Matter

• Chemistry is the study of the composition of matter and how this composition changes through chemical reactions

• Matter is anything that occupies space and has mass

• Matter exists in solid, liquid, and gaseous states

• Within the body, all states or matter are evident

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Basic Chemistry: Energy

• Energy is the capacity to do work or

to put matter into motion

• Kinetic Energy = energy in action

• Potential Energy = stored energy

• Energy form conversions: 1st law of

thermodynamics…

“Neither matter nor energy can be

created or destroyed” 5

Forms of Energy

• Chemical: Stored in chemical bonds

(ex: ATP)

• Electrical: From the movement of

charged particles (ex: nerve impulses)

• Mechanical: Energy directly involved in

moving matter (ex: muscular contraction)

• Radiant/ Electromagnetic: Energy that

travels in waves (ex: Light, UV, X-rays) 6

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Composition of Matter

• All matter is

composed of

elements

• Each element is

composed of atoms

• Each element is has

unique physical &

chemical properties

• Most important for the

body = CHNOPS 7

Atomic Structure

Subatomic

Particle

Characteristics

Proton + charge, large

particle, in

nucleus

Electron - charge, small

particle, around

nucleus

Neutron No charge,

large particle,

in nucleus 8

Atoms of Elements

• Atomic Number = p+

• p+ = e-

• Mass Number = p+ + no

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Chemical Bonding

• e- are arranged in

shells & orbitals

• Valence shell electrons

affect the reactivity of

atoms

• Octet rule

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Molecules & Compounds

• Molecules = two or more chemically bound

atoms

• Two or more atoms of the same element

(ex: H2, O2) = molecule of an element

• Two or more atoms of different elements

(ex: H2O, NaCl) = molecule of a compound

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Ionic Bonds

• e- can transfer & result in ion (charged) formation

• Anions: Negatively charged ion, e- acceptor (Cl-)

• Cations: Positively charged ion, e- donor (Na+)

• Since opposites attract, the atoms stay close

together 12

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Covalent Bonds

• e- are shared in order to fill valence shells part-time

• Covalent bonds involve a shared orbital

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Polarity

• Nonpolar Covalent Molecules:

– Have equal e- pair sharing

– Charge is balanced among atoms

• Polar Covalent Molecules:

– Unequal sharing of e-

– Slight (–) charge on one end, slight (+) charge on another

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Hydrogen Bonds

• Occur when

covalently bonded H

atoms are weakly

attracted by other

atoms

• Not a true bond but is

a weak attraction

• Important for DNA

structure

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Chemical Reactions

• Chemical equations symbolize chemical reactions

• Components: Products & Reactants

• Synthesis: A + B AB

• Decomposition: AB A + B

• Exchange: AB + C AC + B

AB + CD AD + CB

• Some reactions are reversible A + B AB

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Examples

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Factors Affecting Reaction Rates

• Temperature:

Increased = Faster

Decreased = Slower

• Reactant

Concentration:

High = Faster

Low = Slow

• Particle Size:

Small = Fast

Large = Slow

• Catalysts:

Present = Fast

Absent = Slow

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Biochemistry

• Biochemistry: The study of the

chemical composition and reactions of

living matter

• Inorganic Compounds: All compounds

that do not contain carbon (water,

oxygen, salts)

• Organic Compounds: All compounds

that contain carbon (carbohydrates,

lipids, proteins, nucleic acids) 19

Inorganic Compounds: Water

• Most abundant cellular component

• High heat capacity

• High heat of vaporization

• Universal solvent

• Forms hydration layers

• Transports biochemicals

• Reactive

• Cushions 20

Inorganic Compounds: Salts

• Ionic compounds that do

not contain H+ or OH-

• In water, dissociate into

ions/ electrolytes

• Ions are essential for:

– Nerve impulse

transmission (Na, K)

– Muscle contraction (Na,

K)

– Hemoglobin in blood (Fe) 21

Inorganic Compounds: Acids & Bases

• Acids: Donate (release) H+/ protons

– When dissolved in water, acids release H+ and an anion

HCL H+ + Cl-

• Bases: Accept H+, commonly contain OH-

– When dissolved in water, bases release OH- and a cation. The OH- ion then immediately accepts H+ to form water

NaOH Na+ + OH-

OH- + H+ H2O 22

pH Scale

• Measures H+ ion

concentrations

• Acidic:

[H+] > [OH-], pH= 0-6

• Neutral:

[H+] = [OH-], pH= 7

• Basic/ Alkaline:

[H+] < [OH-], pH= 8-14 23

Inorganic Compounds: Buffers

• Buffers: Chemicals that resist abrupt pH

changes

– Function by donating H+ when needed and by

accepting H+ when in excess

– Very, very important for biological systems!!!

H2CO3 HCO3- + H+

weak acid

H+ Donor

weak base

H+ Acceptor

Proton

Rising pH

Drop in pH

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Organic Compounds

• Molecules unique to biological systems

–Carbohydrates

–Lipids (fats)

–Proteins

–Nucleic Acids (DNA & RNA)

• Monomer, Dimer, Polymer

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Building & Breaking Organic

Compounds

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Polymerization

• Chain-like molecules composed of monomeric units

• Continuous dehydration synthesis can grow polymer chains 27