Chapter 2: Chemistry. Basic Chemistry 1. Elements Substances that CANNOT be broken down into simpler substances by chemical processes Represented by symbols.

Chapter 2: Chemistry

Basic Chemistry

1. Elements• Substances that CANNOT be broken

down into simpler substances by chemical processes

• Represented by symbols 1 or 2 letters

Ex: oxygen (O) sodium (Na) chloride (Cl) hydrogen (H)

nitrogen (N) iron (Fe)

2. Compounds• Substances made of 2 or more elements chemically

combined in definite proportions• Represented by formula tells the number & kind of

each atom

Ex: water (H2O) salt (NaCl)

calcium carbonate (CaCO3)

carbon dioxide (CO2)

glucose (C6H12O6)

• Organic compounds contains carbon-hydrogen bonds

Ex: proteins, carbohydrates (CHO), lipids, & nucleic acids

3. Atoms• Smallest unit of matter that still retains the properties of an

element• Building blocks of matter• Subatomic Particles:

  a. Protons (+) charge

- Found in nucleus (center of atom)

  b. Neutrons neutral

- Found in nucleus

c. Electrons (-) charge

- Found outside of nucleus in energy levels

- Always in constant motion

- Important in chemical properties

Atom

Orbital shells

Cont. Basic Chemistry

• Atomic number= number of protons

- Atoms of the same substance have the same atomic number

• Atomic mass= number of protons + number of neutrons

- Concentrated in the nucleus6

CCarbon12.011

Cont. Basic Chemistry

4. Ions• Atoms that have lost or gained electrons• Atoms will lose or gain electrons to achieve stability

outer energy level filled

- 1st ring= maximum of 2 electrons

- Outer shells= lucky #8

a. Anion atoms that gain electrons

- Are negative ions Ex: Cl-, Fl-

b. Cation atoms that lose electrons

- Are positive ions

Ex: K+, Na+, Ca+2

5. Isotopes• Atoms of the same element that have different numbers

of neutrons, but still the same number of protons

- Changes the atomic mass, but not the atomic number

Ex: 3 isotopes of carbon (atomic mass= 6)

12-C, 13-C, 14-C• 50 naturally occurring radioactive isotopes unstable

nucleus that breaks apart giving off radiation• Radioactive isotopes used:

a) to determine age of rocks, fossils, & artifacts

b) as tracers or tags shows where chemical reactions are occurring (PET)

c) to preserve food & treat cancer

Isotopes

Nonradioactive carbon-12 Nonradioactive carbon-13 Radioactive carbon-14

6 electrons6 protons6 neutrons

6 electrons6 protons7 neutrons

6 electrons6 protons8 neutrons

Chemistry of Carbon

1. Organic compounds

- Contains carbon-hydrogen bonds

2. Inorganic compounds

- No carbon-hydrogen bonds

• CARBON (atomic structure) reactive (unstable) atom

- Must make 4 bonds to become stable

- May bond w/ itself or other atoms in many ways, forming many kinds of organic compounds

found in living things

Ex: CHO, fats, proteins, nucleic acids

Formulas

1. Molecular Formula• List elements present• Shows number of atoms for each element

Ex: CH4, C6H12O6

 2. Structural Formula• List elements present• Shows number of atoms for each element• Show shape or pattern or arrangement of atoms

methane

Chemical Bonding

• Force of attraction (energy) holding 2 atoms together

• Occurs when needed to fill outer orbits unstable atoms tend to react until they become stable

• 3 types: 

1. Covalent bonds

- Sharing a pair of electrons

- Must have overlapping orbits between atoms

- Shown by lines connecting atoms in a formula

Covalent Bonding

Cont. Chemical Bonding

2. Ionic bonds

- Must involve a transfer of electrons

- One atom loses an electron (+), while other gains an electron (-)

- Bond will form between 2 oppositely charged ions

- Shown by charge signs on ions of molecular formula

Ex: Na+Cl-

Ionic Bonding

Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl-)

Protons +11Electrons -11Charge 0

Protons +17Electrons -17Charge 0

Protons +11Electrons -10Charge +1

Protons +17Electrons -18Charge -1

3. Hydrogen bonds

- Links molecules together rather than atoms

- Like a “molecular magnet” with (+) and (-) portions

- Weak bonds short distances between molecules

- Found in polar molecules (like H2O) have areas of charge

- Symbolized by H- - - - (dotted lines)

Cont. Hydrogen bonds

- Help to form shape of important biological molecules (DNA & protein)

- Exhibits:

a. Cohesion degree of “stickiness” between identical molecules

b. Adhesion degree of “sticking” to different molecules

c. Surface tension related to cohesion/ a measure of how difficult it is to stretch/ break the surface of a liquid

Properties of Water

Adhesion  Cohesion Surface Tension 

Electrolytic Solutions

•  Two kinds of ionic compounds dissolved by H2O

1. Acids excess hydrogen ions (H+)

ex: HCl H+ + Cl-

2. Basesexcess hydroxide ions (OH-)

ex: NaOH Na+ + OH-

• When an acid & base are mixed, they tend to neutralize each other by producing a salt

ex: HCl + NaOH H2O + NaCl

acid base water salt

Cont. Electrolytic Solutions

• Various indicators tests used to determine if solutions are acidic, basic, or neutral & some measure the strength more quantitatively

1. Taste 4. Feel

2. Litmus paper 5. Indicator solutions

3. pH paper 6. pH meters

Cont. Electrolytic Solutions

• Hydrogen ion concentrations (pH scale)

- System of measuring strength of acids & bases

- Requires use of pH paper, pH color chart, pH scale 

Red Strong acid Weak acid Green Weak Base Strong base Purple

1 ---------------------------------------------7-----------------------------------------------14

ACID NEUTRAL BASE

H+ ←---------------------------------- H+ = OH- -----------------------------------→ OH-

More H+ less OH- More OH- less H+

- Organisms vary in their response to the pH of their environment most living things exist w/in very narrow ranges (usually between 6 & 8)

- Extreme values damage tissues & enzymes and link

Oven cleaner

Bleach

Ammonia solution

Soap

Sea water

Human bloodPure waterMilkNormalrainfall

Acid rainTomatojuice

Lemon juice

Stomach acid

NeutralIncreasingly Basic

Increasingly Acidic

Section 2-2

pH Scale

pH Scale

Cont. Ch 2: Organic Molecules

Size of Organic Molecules

• Large organic molecules:

1. Carbohydrates (CHO)

2. Proteins

3. Lipids (Fats)

4. Nucleic Acids•  All are found in living things• All are made up of many small repeating

molecules (monomers) added to make a larger molecule (polymer)

Cont. Size of Organic Molecules• All are made up of many small repeating molecules

(monomers) added to make a larger molecule (polymer)

• Small units (building blocks) form larger units (macromolecules)

Ex: monomer + monomer + monomer + monomer + etc = polymer

 • Small repeating units are put together to make something

larger

Ex: like many small bricks make up a brick wall

like many small cells make up an organism

like many small molecules make up a larger molecule

like many simple sugars make up a carbohydrate

Processes That Change Size of Organic Molecules

1. Dehydration Synthesis (Condensation)• “Building”• Adding small molecules together to form a larger

molecule

• H2O is removed (formed) between 2 building blocks

• Energy MUST be addedEx:

sucrose

Dehydration

• Ex: Photosynthesis

6 CO2 +12 H2O C6H12O6 + 6 H2O + 6 O2

OR

Glucose Glycogen

Cont. Processes That Change Size of Organic Molecules

2. Hydrolysis • “Splitting”• Larger molecule is broken down into smaller

molecules

• H2O must be added to split 2 building blocks

• Energy is released

  Ex: Respiration

  C6H12O6 + 6H2O + 6 O2 6CO2 +12H2O

OR

Glycogen Glucose

Macromolecules (4)

1. CARBOHYDRATES (CHO)• Starches/ complex sugars• Basic energy source for life• Made up of carbon, hydrogen, & oxygen

a. 2 H for every C

b. 1 H2O for every C

C: H: O

1: 2: 1

  (CH2O)n

CHO• Building blocks of CHO

Simple sugars

- Formula for simple sugar= C6H12O6

• Isomers same formula, different structure

• - 3 isomers of C6H12O6 glucose, fructose, & galactose

• Most sugars end in “ose”

• Types of sugars:

a. Monosaccharides

- Simple sugars C6H12O6

Ex: glucose, fructose, galactose

also ribose C5H10O5 & deoxyribose C5H10O4

- Used for fuel, converted to other organic molecules, or combined into polymers

Synthesis of a Disaccharide

b. Disaccharides

- Double sugars C12H22O11

1. Maltose (malt sugar) = glucose + glucose

2. Sucrose (table sugar) = glucose + fructose

3. Lactose (milk sugar) = = glucose + galactose

Synthesis of A Polysaccharide

c. Polysaccharides

- Complex sugars

1. Cellulose plant cell walls

2. Glycogen animal starch (stored in liver & muscle cell)

3. Plant starch stored in plant vacuoles

4. Chitin exoskeletons of insects & crustaceans

Starch vs Cellulose

Starch

Glucose

Section 2-3

Figure 2-13 A Starch

STARCH 

Cellulose

Glycogen

Cont. Macromolecules

2. PROTEINS- consists of 1 or more folded polypep. each folded into a specific 3D structure

• Polypeptides a chain of many amino acids• Makes up cell parts (membrane), cell enzymes, collagen,

& some hormones account for variations between individuals of the same species, nutrients- provide energy

• Made up of carbon, hydrogen, oxygen, & nitrogen

• Building blocks of proteins Amino Acids (AA)

- 20 different AA in living things

- All AA have 3 identical parts: [*]

a. [*] Amino group (-NH2)

b. [*] Acid group (-COOH) aka “carboxyl” group

c. [*] Central carbon w/ hydrogen (--C-H)

d. R (radical) group varies

Amine group (basic)

Carboxyl group (acidic)

Radical group – can be substituted to form other proteins

Central C-H group

General structure Alanine Serine

Section 2-3

Figure 2-16 Amino Acids

Amino group Carboxyl group

AMINO ACIDS

Cont. Proteins

Peptide bond - Special bond formed between 2 AA- between the amino group of 1 AA & the acid group of the other AA

Peptide Bond Formation

Levels of Protein Structure

a. Primary structure- unique sequence AA (polypeptide)

b. Secondary structure- alpha helix shape or beta sheets

c. Tertiary structure- folding/ bond break easily w/ acid/ heat

d. Quaternary structure- 2/ more polypeptides

Aminoacids

Section 2-3

Figure 2-17 A Protein

A PROTEIN

Protein

• Forms unlimited kinds of proteins (tremendous variety in protein structure)

a. Kinds of AA

- 20 kinds combined in different combinations

b. Number of AA

- 1 protein may have 99 AA, another 300+

c. Sequence/ order of AA

Ex: glycine, alanine alternating or alanine, glycine alternating or all valine

d. Protein type determined by DNA (genes)

 • Essential amino acids

- 12 essential AA

- Cannot make in the body & must take in daily in our diet

Cont. Proteins•  Proteins may be

damaged by heat & acid causes them to change shape

- Denaturation once shape has changed no longer functions / irreversible process!

Ex: raw egg white + heat opaque egg white

Cont. Macromolecules

3. LIPIDS • Fats- triglyceride, oils, waxes; also phospholipids,

cholesterol, steroids, & chlorophyll• Used for building cell parts & for energy reserve• Made up of carbon, hydrogen, & oxygen (no specific

ratio) hydrocarbons• Building blocks for fats Triglyceride= 1 glycerol + 3 fatty

acid chains (14-20 CH2)

Triglyceride

Cont. Lipids

• Types of fat:

a. Saturated Fats

- “Bad fats”

- Every carbon is filled w/ hydrogen

- NO double bonded carbons

- Solid at room temperature

- Animal fat/ lard hard to mix w/

H2O

Cont. Lipids

 b. Unsaturated Fats

- “Good fats”

- Some carbons do NOT have hydrogens

- 1 or more double bonded carbons

- Liquid at room temperature

- Vegetable/ fish oils

Fats

What type of fat is this?

Phospholipid

• Similar to fat has only 2 fatty acids attached to glycerol instead of 3

• 3rd hydroxyl group of glycerol is joined by phosphate group

• Amphipathic- has polar (hydrophilic) & nonpolar regions (hydrophobic)

• Major component of ALL cell membranes

Phospholipid

Lipid Bilayer

Steroids• Characterized by 4 fused rings of carbon atoms

•Cholesterol common component of animal cell membranes & production of sex hormones• Vitamin D

Cont. Macromolecules

4. NUCLEIC ACIDS• Used to control cell activities

Ex: protein synthesis• Carries genetic (hereditary) information• Composed of carbon, hydrogen, oxygen, nitrogen, and

phosphorus• Building blocks of nucleic acids Nucleotides= sugar +

nitrogen base + phosphate

Nucleotide

Nucleic Acid

Cont. Nucleic Acids

• Types of nucleic acids:

a. DNA (deoxyribonucleic acid)

- Found mainly in the nucleus

- Deoxyribose sugar

b. RNA (ribonucleic acid)

- Found in both nucleus & cytoplasm

- Ribose sugar

Cont. Macromolecules

5. ENZYMES• All are proteins• Used as catalysts to start chemical reactions

- Lower the amount of activation energy needed w/o increasing heat

 • Composed of carbon, hydrogen, oxygen, &

nitrogen

Cont. Enzymes

• Are specific 1 enzyme for each reaction• Active site specific part that matches

shape w/ a substance “substrate” that enzyme acts on

• Often ends in “ase”

- maltase, lipase, amylase, lactase

Enzyme Reaction

CarbonCompounds

include

that consist of

which contain

that consist of that consist of that consist of

which contain which contain which contain

Section 2-3

Concept Map

Carbohydrates Lipids Nucleic acids Proteins

Sugars and starches

Fats and oils Nucleotides Amino Acids

Carbon,hydrogen,oxygen

Carbon,hydrogen,oxygen

Carbon,hydrogen,oxygen, nitrogen,

phosphorus

Carbon,hydrogen,oxygen, 

nitrogen,

OVERVIEW OF MACROMOLECULES

HUMAN CHORIONIC GONADOTROPIN (hCG)

1. Primary Structure- Order of AAs held together by peptide bonds (10 AAs)

Glutamine- Histidine- Tryptophan- Serine- Histidine- Glycine (*)- Leucine (*)- Serine- Proline- Glycine (*)

Glutamine- blue Glycine- orangeHistidine- red Leucine- yellowTryptophan- clear Proline- pinkSerine- green

2. Secondary Structure- Alpha Helix Coils or Beta Pleated Sheets (due to H-bonds)

3. Tertiary Structure- Overall folding/ conformation of polypeptide (H-bonds/ wk bonds

4. Quarternary Structure- 1 or more strands of polypeptides coming together