Fundamentals of Chemistry

Chapter 2

What Are Atoms?

• Smallest particles that retain properties of an element, smallest particle of a substance

• Made up of subatomic particles:

– Protons (+)

– Electrons (-)

– Neutrons (0) no charge)

Elements

• Fundamental forms of matter

• Can’t be broken apart by normal means

• 92 occur naturally on Earth

Most Common Elements in Living Organisms

Oxygen

Hydrogen

Carbon

Nitrogen

Representing the Hydrogen Atom

electron

proton

electron

Shell model Ball model Electron density cloud

Atomic Number and Mass

• # = Number of protons

• All atoms of an element have the same atomic number

• Mass= # of P + # on N

1.0079 ----- Atomic Mass

H element symbol

1 --- Atomic number

Mass Number

Number of protons

+Number of neutrons

Isotopes vary in mass number

# of protons = # of electrons

Isotopes

• Atoms of an element with different numbers of neutrons (different mass numbers)

• Carbon 12 has 6 protons, 6 neutrons

• Carbon 14 has 6 protons, 8 neutrons

What Determines whether Atoms Will Interact?

The number and arrangement of their electrons

Electrons

• Carry a negative charge

• Repel one another

• Are attracted to protons in the nucleus

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

Shell Model

• First shell

– Lowest energy

– Holds 1 orbital

with up to 2

electrons

• Second shell

– 4 orbitals hold

up to 8

electrons HYDROGEN1p+ , 1e-

HELIUM2p+ , 2e-

CARBON6p+ , 6e-

OXYGEN8p+ , 8e-

SODIUM11p+ , 11e-

CHLORINE17p+ , 17e-

Chemical Bonds, Molecules, & Compounds

• Bond is union between electron structures of atoms

• Atoms bond to form molecules• Molecules may contain atoms of only

one element - O2

• Molecules of compounds contain more than one element - H2O

• Compound= +/- atoms

Important Bonds in Biological Molecules

Ionic Bonds

Covalent Bonds

Hydrogen Bonds

Ionic Bonding

• One atom loses electrons, becomes positively charged ion

• Another atom gains these electrons, becomes negatively charged ion

• Charge difference attracts the two ions to each other

Covalent Bonding

Atoms share a pair or pairs of electrons to fill outermost shell

•Single covalent bond

•Double covalent bond

•Triple covalent bond

Nonpolar Covalent Bonds

• Atoms share electrons equally

• Nuclei of atoms have same number of protons

• Example: Hydrogen gas (H-H)

Polar Covalent Bonds

• Number of protons in nuclei of participating atoms is not equal

• Electrons spend more time near nucleus with most protons

• Water - Electrons more attracted to O nucleus than to H nuclei

Hydrogen Bonding

• Molecule held together by polar covalent bonds has no net charge

• However, atoms of the molecule carry different charges

• Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule

Examples of

Hydrogen Bonds

hydrogenbond

water molecule

ammonia molecule

Properties of Water

Polarity

Temperature-Stabilizing

Solvent

Cohesive

Surface tension

Water Is a Polar Covalent Molecule

• Molecule has no net charge

• Oxygen end has a slight negative charge

• Hydrogen end has a slight positive charge

+ +

HH

O

Water Is a Good Solvent

• Ions and polar molecules dissolve easily in water

• When solute dissolves, water molecules cluster around its ions or molecules and keep them separated

Water Cohesion• Hydrogen bonding holds

molecules in liquid water together

• Creates surface tension

• Allows water to move as continuous column upward through stems of plants

Na+

Cl–

– –

––

––

–

––

– –

+ ++

+

+

+

+

+

+

+

+

++ +

+

+

+

+

Spheres of Hydration

The pH Scale

• Measures H+ concentration of fluid• Change of 1 on scale means 10X

change in H+ concentration

Highest H+ Lowest H+

0---------------------7-------------------14Acidic Neutral Basic

Examples of pH

• Pure water is neutral with pH of 7.0

• Acidic– Stomach acid: pH 1.0 - 3.0

– Lemon juice: pH 2.3

• Basic– Seawater: pH 7.8 - 8.3

– Baking soda: pH 9.0

The pH Scale

Acids & Bases

• Acids

– Donate H+ when dissolved in water

– Acidic solutions have pH < 7

• Bases

– Accept H+ when dissolved in water

– Acidic solutions have pH > 7

Organic CompoundsHydrogen and other elements covalently bonded to carbon

** The Biomolecules

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

Carbohydrates

Monosaccharides(simple sugars)

Oligosaccharides(short-chain carbohydrates)

Polysaccharides(complex carbohydrates)

Monosaccharides

• Simplest carbohydrates

• Most are sweet tasting, water soluble

• Most have 5- or 6-carbon backbone

Glucose (6 C) Fructose (6 C)

Ribose (5 C) Deoxyribose (5 C)

Polysaccharides

• Straight or branched chains of many sugar monomers

• Most common are composed entirely of glucose– Cellulose

– Starch (such as amylose)

– Glycogen

Lipids

• Most include fatty acids– Fats– Phospholipids– Waxes

• Sterols and their derivatives have no fatty acids

• Tend to be insoluble in water

Fats

• Fatty acid(s) attached to glycerol

• Triglycerides are most common

• Carboxyl group (-COOH) at one end

• Carbon backbone (up to 36 C atoms)

– Saturated - Single bonds between carbons

– Unsaturated - One or more double bonds

Sterols and Derivatives

• No fatty acids

• Rigid backbone of four fused-together

carbon rings

• Cholesterol - most common type in

animals

Properties of Amino Acids

• Determined by the “R group”

• Amino acids may be:

– Non-polar

– Uncharged, polar

– Positively charged, polar

– Negatively charged, polar

Primary Structure & Protein Shape

• Primary structure influences shape in two main ways:– Allows hydrogen bonds to form between

different amino acids along length of chain

– Puts R groups in positions that allow them to interact

Secondary Structure

• Hydrogen bonds form between different parts of polypeptide chain

• These bonds give rise to coiled or extended pattern

• Helix or pleated sheet

Tertiary Structure

• Folding as a result of interactions between

R groups

Quaternary StructureSome proteins are made up of more than one

polypeptide chain

Nucleotide Structure

• Sugar

– Ribose or deoxyribose

• At least one phosphate group

• Base

– Nitrogen-containing

– Single or double ring structure

Nucleic Acids

• Composed of nucleotides

• Single- or double-stranded

• Sugar-phosphate backbone

DNA and RNA

** DNA ---Double-stranded • Consists of four types of nucleotides• A bound to T C bound to G

** RNA --- Usually single strands, • Four types of nucleotides

• Unlike DNA, contains the base uracil in place

of thymine

• Three types are key players in protein synthesis