Chapter 2: Chemistry

Comes Alive

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

Structural Organization: Chemical Level

• Atoms/ Elements

• Molecules/

Compounds

• Macromolecules

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

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”

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)

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

Atomic StructureSubatomic

ParticleCharacteristics

Proton + charge, large particle, in nucleus

Electron - charge, small particle, around nucleus

Neutron No charge, large particle, in nucleus

Atoms of Elements

• Atomic Number = p+

• p+ = e-

• Mass Number = p+ + no

Chemical Bonding

• e- are arranged in shells & orbitals

• Valence shell electrons affect the reactivity of atoms

• Octet rule

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

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

Covalent Bonds

• e- are shared in order to fill valence shells part-time• Covalent bonds involve a shared orbital

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

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

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

Examples

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

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)

Inorganic Compounds: Water

• Most abundant cellular component

• High heat capacity• High heat of vaporization• Universal solvent• Forms hydration layers• Transports biochemicals• Reactive• Cushions

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)

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

pH Scale

• Measures H+ ion concentrations

• Acidic:

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

• Neutral:

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

• Basic/ Alkaline:

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

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 acidH+ Donor

weak baseH+ Acceptor

Proton

Rising pH

Drop in pH

Organic Compounds

• Molecules unique to biological systems– Carbohydrates

– Lipids (fats)

– Proteins

– Nucleic Acids (DNA & RNA)

• Monomer, Dimer, Polymer

Building & Breaking Organic Compounds

Polymerization

• Chain-like molecules composed of monomeric units

• Continuous dehydration synthesis can grow polymer chains