Download Chapter 2: Chemistry

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 carbonhydrogen 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 nucleus
6
C
Carbon
12.011
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-, Flb. 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
6 electrons
6 protons
6 neutrons
6 electrons
6 protons
7 neutrons
Radioactive carbon-14
6 electrons
6 protons
8 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)
Protons +11
Electrons -11
Charge
0
Protons +17
Electrons -17
Charge
0
Sodium ion (Na+)
Protons +11
Electrons -10
Charge +1
Chloride ion (Cl-)
Protons +17
Electrons -18
Charge -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+ + Cl2. Basesexcess 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- -----------------------------------→ OHMore H+ less OHMore 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
pH Scale
pH Scale
Section 2-2
Increasingly Basic
Oven cleaner
Increasingly Acidic
Neutral
Bleach
Ammonia solution
Soap
Sea water
Human blood
Pure water
Milk
Normal
rainfall
Acid rain
Tomato
juice
Lemon juice
Stomach acid
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 added
Ex:
 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
Figure 2-13 A Starch
Section 2-3
STARCH
Starch
Glucose
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
Central C-H group
Amine
group
(basic) 
 Carboxyl
group (acidic)
Radical group – can be substituted to form other
proteins
Figure 2-16 Amino Acids
Section 2-3
Amino group
AMINO ACIDS
Carboxyl group
General structure
Alanine
Serine
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 structurealpha helix shape or beta
sheets
c. Tertiary structure- folding/
bond break easily w/
acid/ heat
d. Quaternary structure- 2/
more polypeptides
Figure 2-17 A Protein
Section 2-3
A PROTEIN
Amino
acids
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
Concept Map
OVERVIEW OF MACROMOLECULES
Section 2-3
Carbon
Compounds
include
Carbohydrates
Lipids
Nucleic acids
Proteins
that consist of
that consist of
that consist of
that consist of
Sugars and
starches
Fats and oils
Nucleotides
Amino Acids
which contain
which contain
which contain
which contain
Carbon,
hydrogen,
oxygen
Carbon,
hydrogen,
oxygen
Carbon,hydrogen,
oxygen, nitrogen,
phosphorus
Carbon,
hydrogen,oxygen,
nitrogen,
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
Histidine- red
Tryptophan- clear
Serine- green
Glycine- orange
Leucine- yellow
Proline- pink
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