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
• 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