Chemical Level of OrganizationChapter 2

Atoms, Molecules and Bonds

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

P and S

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

Formation of NaCl

• Sodium atom (Na) – Outer shell has one electron

• Chlorine atom (Cl) – Outer shell has seven electrons

• Na transfers electron to Cl forming Na+ and Cl-

• Ions remain together as NaCl

Covalent Bonding

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

•Single covalent bond

•Double covalent bond

•Triple covalent bond

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

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

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

Glycogen

• Sugar storage form in animals

• Large stores in muscle and liver cells

• When blood sugar decreases, liver cells degrade glycogen, release glucose

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

Protein Synthesis

• Protein is a chain of amino acids linked by

peptide bonds

• Peptide bond

– Type of covalent bond

– Links amino group of one amino acid with carboxyl

group of next

– Forms through condensation reaction

Protein Shapes

• Fibrous proteins

– Polypeptide chains arranged as strands or sheets

• Globular proteins

– Polypeptide chains folded into compact, rounded

shapes

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

Polypeptides with Attached Organic Compounds

• Lipoproteins

– Proteins combined with cholesterol,

triglycerides, phospholipids

• Glycoproteins

– Proteins combined with oligosaccharides

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

• 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