(About 10 exam questions will come from Chapter 1)
A. Definition of Life:
1. Organization: Atoms (Subatomic
Particles Chapter 2)
Molecules
(Inorganic (water, salts) vs.
Organic
(contain carbon))
Macromolecules: Carbohydrates (sugars,starches)
Proteins
Lipids
Nucleic
Acids (DNA, RNA)
Cells
Tissues: Epithelial
Connective
Muscle
Nervous
Organs: Heart
Liver
Kidney
(many more)
Systems: Circulatory
Digestive
Skeletal
(moreŠ)
Organism: 5 Kingdoms
Also:
(not on exam) Species
Population
Community
Ecosystem
Biosphere
*The whole is greater than
the sum of its parts: each level
of organization has new properties (functions, requirements) not accounted for
by summing the parts of the previous levels
2. Acquisition of Materials and Energy
- Materials: most important is organic
nutrients (food)
- Food provides building blocks for
cellular (organic) macromolecules
and energy (the ability to
do work)
ATP: source of energy for chemical reactions in cell
Couple
endothermic reaction to exothermic reaction (ATP hydrolysis: ATP Þ ADP + PI)
Metabolism: all the
chemical reactions in a cell
*Homeostasis:
maintenance of internal conditions
3. Response to stimuli
-
Find energy and
nutrients
-
Survival (escape from
predators)
4. Reproduction and Development
- Reproduction: survival of the species
Asexual:
Bacteria and Protists
Sexual: Higher organisms
(most Fungi, Plants and Animals)
5. Adaptation
- modifications to help an organism survive in its environment
Evolution: descent
with modification one species gives
rise to several
different species, each adapted
to its environment and way of life.
Taxonomy: identification
and classification of organisms according to similar characteristics
:Linnaeus: Binomial
Nomenclature: scientific name for
organism = genus + species
names
5 Kingdoms & characteristics of each (some overlap with Lab)
prokaryote vs. eukaryote
Scientific Method: Steps
(p. 11) - Know how to apply steps to experiment
Controlled experiment: Control group (or negative control)
Reviewing the Chapter (p. 16 always a good idea) & Testing Yourself #1-4, 5,7,8,9,11
Chapter 2: Chemistry
(About 15 exam questions will
come from Chapter 2)
All matter is composed of elements
-
Matter: anything that has mass and takes up
space solid, liquid or gas
- Elements: present
in both living & nonliving matter
92 elements are
naturally-occurring
Hydrogen
Nitrogen
Phosphorus
Sulfur
Atom:
the smallest part of an element that retains all of its properties.
- only 1
type of atom in each element
-
composed of subatomic particles: proton positive
charge
electron negative
charge
neutron neutral
charge
- Atomic number = # of protons in the nucleus of an atom
- Atomic weight = # of protons + # of neutrons in the nucleus of an
atom (weight of electron
is negligible)
- # protons = # electrons for a given
atom
-
Isotopes: atoms
with the same atomic number, but different atomic weights (i.e.: different # of neutrons)
- Examples: 12C,
13C, 14C
- Radioactive Isotopes: unstable isotopes that emit radiation in the form of radioactive particles or radiant energy when they decay
Chemical properties of atoms:
Bohr Model: electrons orbit in concentric energy levels (electron shells) about the nucleus of an atom
Electrons of an atom differ in amount of potential (stored) energy
- electrons closest to the nucleus have the least potential energy
(nonbonding electrons)
- electrons farthest from the nucleus have the greatest potential
energy (valence or bonding electrons)
Bohr Model (cont.):
First energy level can contain a maximum of 2 electrons
Second energy level, and all additional energy levels, can contain a maximum of 8 electrons
Octet rule: except for the first energy level, the outermost energy level is most stable when it has 8 electrons (the first energy level is most stable with its maximum of 2 electrons)
Electrons occupy orbitals within energy levels
- each orbital can contain a maximum of 2 electrons
- the first energy level has 1 orbital (maximum 2 electrons), the
second energy level has 4 orbitals (maximum 8 electrons)
Bonding:
Compound: 2 or more elements bonded together
Molecule: smallest part of a compound that retains all of its properties
1. Ionic Bonding: transfer of electrons from one atom to another
- results in ions: charged particles resulting from charge imbalance (greater or fewer electrons than protons) due to electron transfer
- Examples: NaCl,
MgCl2, Na2O
- Chemical formulas of compounds based on
# of valence electrons
(example: from above: MgCl2, Mg has 2
valence electrons to donate, while Cl can
only accept 1, so two Cl atoms are needed to accept the 2 valence electrons
donated by one Mg atom)
2. Covalent bonding: sharing of electrons between 2 or more atoms
- each atom acquires an octet of valence
electrons (electrons in
outermost shell)
Orbital
overlap: outer orbitals from 2 atoms overlap to share electrons
Examples: CH4, O2, H2,
C6H12O6
Oxidation: loss of
electrons or H atoms
Reduction: gain of
electrons or H atoms
Polar Covalent bond: unequal sharing of electrons between atoms in a
covalent bond (eg: water, H2O)
-due to difference in electronegativities of atoms in bonds
-more electronegative
atom has slight negative charge, less
electronegative atom has slight positive charge
-asymmetrical differences lead to polar molecules
Hydrogen Bonding:
-bond between a slightly positive hydrogen atom of one molecule, and a slightly negative atom (usually oxygen or nitrogen)of the same or another molecule
-weak bonding compared to ionic and covalent bonding, but
many bonds increases strength
-good example is water
molecules
Properties of Water:
1. resists changes in temperature (in part due to hydrogen bonding)
-calorie: amount
of energy required to raise temperature of 1 gram of water by 1 degree Celsius
-other
covalently bonded liquids require about half this energy
-important
for organisms (mostly water): maintains normal internal temperatures
(homeostasis)
2. Water
has a high heat of vaporization
-high
boiling point (100 degrees Celsius)
-heat
of vaporization (energy required to convert water to steam) is 540 calories
(very high)
-energy
needed to break hydrogen bonds
3. Water is the universal solvent:
-many
compounds dissolve in water
(separate into ions)
a. ionic compounds : salts
b. polar covalent
compounds
Water is a polar molecule:
the negative ends of water molecules are
attracted to positively charged
ions, and the positive ends of water
molecules are attracted to
negatively charged ions
-Hydrophilic molecules (ionic compounds) attract water
- Hydrophobic molecules
(nonionized, nonpolar) molecules cannot
attract water
Properties of Water
(cont.):
4. Water molecules are cohesive and adhesive
-Cohesive:
water molecules are attracted to
other water molecules
-Adhesive:
water molecules are attracted to
other substances (polar surfaces)
5. Water has high surface tension: due
to hydrogen bonding (strengthens interactions)
6. Frozen water is less dense than liquid water
-water expands upon freezing
pH scale (power of hydrogen): indicates acidity or basicity of
solution
-ranges from 0 (strong acid)
to 14 (strong base); pH=7 is neutral
-water ionizes to release hydrogen ions and hydroxide ions
Acid:
molecules that release hydrogen ions (H+) when dissolved in
water
-acids are hydrogen ion
donors
Base:
molecules that release hydroxide (OH-) ions , or increase the
number of hydroxide ions available, when dissolved in water
-bases are hydrogen ion
acceptors
Chapter 2 (cont.)
Buffers: maintain
stable pH of solution (resist changes in pH)
-normal pH of blood is 7.4
-Buffers can take up excess
hydrogen or hydroxide ions
-Buffers have acidic and basic
component
-Blood uses carbonic acid (acidic) bicarbonate ion (basic) buffer system
-Bicarbonate ions take up
added hydrogen ions, and carbonic acid takes up
excess hydroxide ions
(This is the toughest chapter in the book to narrow down to the most important pointsŠ I¹ll try to get a revised (shorter) version out in the next day or so (check back at the site). For now, focus on the basic definitions. Keep in mind that approximately one half of the exam (20-25 questions) will come from this chapter.)
Cells Contain Organic
Molecules (and inorganic molecules)
Organic Molecules: Carbon-based molecules
- Carbon
atoms are bonded mainly to atoms of hydrogen, oxygen,
and nitrogen, as well as some other atoms
- Always contain carbon and hydrogen
- Always covalent-bonding
Inorganic
Molecules: Molecules which do not contain carbon and hydrogen (e.g.:
salts, strong acids and bases, metal compounds)
- usually ionic-bonding
All living things contain the same classes of primary molecules: Carbohydrates
Functional
Groups: groups of atoms that always behave in a particular manner
when bonded together
Organic
molecules composed entirely of carbon
and hydrogen are always hydrophobic
molecules (not attracted to water)
-
the addition of an ionizable functional group (usually a group that can give up or accept a hydrogen atom) makes an organic molecule hydrophilic (attracted to water)
-
many functional groups (hydroxyl, ketone, amine) do not ionize completely
(all molecules do not form positive or negative ions by releasing or accepting
a hydrogen atom), yet still retain polar/hydrophilic nature in water
Please Note: Structures will NOT be on the examŠ they are here for reference
only. For these, know the
functional groups present in each macromolecule (e.g.: Carbohydrates contain
hydroxyls, ketones, & aldehydes).
Organic
molecules and their common
functional groups:
(note: R group is always the remainder of the organic molecule being considered; functional
group is in bold)
Organic
Molecule Functional
Group Structure Examples
Carbohydrates: hydroxyl (alcohol) R
OH all sugars
(glucose,
fructose, etc.)
O
| | some
sugars
ketone R C R (fructose)
/
/
aldehyde R
C some sugars
\ (glucose)
O
/ /
Proteins: carboxyl (acid) R C all amino acids
\
H
/
amine (amino) R
N all amino acids
\
H
sulfhydryl R
SH some amino
acids (cysteine)
Organic molecules and their common functional groups:
Organic Molecule Functional Group Structure Examples
Lipids: carboxyl (acid) see proteins all fatty acids
O
| |
phosphate R
O P OH phospholipids
|
Nucleic
acids: phosphate see lipids all nucleic acids
Also: Some proteins have amino acids with hydroxyl groups
All
nucleic acids have a
5-carbon sugar (ribose) with hydroxyl & aldehyde groups
Many,
many more modifications of organic molecules with one or more of the above
functional groups to serve some specific function in the cell
The
diversity of organic molecules in
organisms is due to:
-
Isomers:
molecules with identical molecular
formulas, but different structures
(e.g.: glucose, fructose, & galactose (among other 6-carbon sugars)
-
Multiple types of subunits: - 4
nitrogenous bases in nucleic acids (A, C, G, T/U)
- 20+
different amino acids in proteins
-
saturated or unsaturated fatty acids in lipids
- sugar
isomerization and modification in
carbohydrates
-
Branching (carbohydrates), Folding (proteins), Packaging (nucleic acids)
(e.g.:
secondary, tertiary, & quaternary structure in proteins)
Organic
macromolecules in cells have
specific subunits
- The subunit is a monomer
- The macromolecule is a polymer, or a chain, of monomers
- The monomers in a polymer can be
the same type, or different types, of subunit
Remember: there
are 20+ different amino acid monomers, and 4 nucleotide monomers (for
both DNA and RNA), as well as many different fatty acids (both saturated and unsaturated) in plants and
animals and many different monosaccharide isomers (12+ isomers of
glucose)
Monomer Polymer
Monosaccharide Polysaccharide
Glycerol
+ 3 fatty acids Lipid
Amino
acid Protein
Nucleotide Nucleic
acid
Organic
macromolecules are built up by condensation & broken down by hydrolysis
-
Monomer subunits are added to growing chains of organic macromolecules
by condensation reactions: formation of a bond with removal of water
-
Monomer subunits are removed from chains of organic macromolecules
by hydrolysis reactions: breaking of a bond by the addition of water
Carbohydrates: (contain
carbon, hydrogen, and oxygen atoms)
Monosaccharides: simple
sugars with a backbone of 3 to 7 carbon atoms
Glucose is a 6-carbon sugar (hexose) found in the blood of animals, and Fructose is a hexose found in fruits
Ribose is a 5 carbon sugar (pentose) found in RNA (in DNA, the pentose
sugar is deoxyribose)
Disaccharides: 2 monosaccharides joined by condensation
Maltose (a disaccharide in the digestive tract) = glucose
+ glucose
Lactose ( a disaccharide in milk) = glucose + galactose (another hexose)
Sucrose (a disaccharide in fruits & vegetables) =
glucose + fructose
Polysaccharides: chains
of (usually the same or repeating) monosaccharides
-
chains can be
unbranched, slightly branched, or highly branched
Polysaccharides:
1. Glycogen
is a highly branched polymer of glucose, and is the storage form of carbohydrates in animal
cells
2. Starch is
a more moderately branched polymer of glucose, and is the storage form of carbohydrates in plant
cells
3. Cellulose is
an unbranched polymer of glucose, with adjacent chains held together by hydrogen
bonds, giving it a very rigid
structure. It is the major
structural component of plant cell walls
4. Chitin is
a polymer of modified glucose monomers.
In chitin, the modified
glucose has attached amino and acetyl (-COCH3) groups (N-acetyl-glucosamine). Chitin is a very rigid polysaccharide
found in the exoskeletons of crustaceans (like crabs)
Lipids:
The
monomer in lipids is the triglyceride
One
triglyceride = Glycerol + 3 fatty acids
- Glycerol has 3 carbon atoms and 3 hydroxyl groups
-
Fatty acids have a long hydrocarbon
(carbon + hydrogen) chain with a carboxylic acid group at one end
- Condensation joins a fatty acid to each of the hydroxyl groups in
glycerol
- Both fats and oils are composed
of triglycerides
-
The condensation reaction removes the ionizable functional groups from
fatty acids and glycerol; hence, these molecules are very hydrophobic
In
animal cells, lipids are in the
form of fats
- fats are solid at room
temperature
-
fatty acids in fats are saturated: each carbon atom in the fatty acid molecules have
the maximum number of bonded hydrogen atoms (each carbon is saturated with hydrogen atoms); there are no C=C double bonds
In
plant cells, lipids are in the
form of oils
- oils are liquid at room
temperature
-
fatty acids in fats are unsaturated: one or more carbon atoms in the fatty acid molecule
has less than the maximum number of bonded hydrogen atoms; there are one
or more C=C double bonds
Waxes
= long chain fatty acid molecules
bonded to alcohols (R OH)
-
waxes usually serve some structural or protective function (e.g.: prevention of water loss in plants,
protection of the eardrum in animals, formation of bees¹ honeycombs)
Phospholipids = Glycerol + 2 fatty acids + 1 polar (phosphate-containing) head group (instead of
third fatty acid in triglyceride)
-
allows molecules to have hydrophobic end (2 fatty acids) and hydrophilic (phosphate) end
-
these molecules are the subunits of biological membranes in
cells (e.g.: plasma membrane): the
polar head group is in contact with water on the inside and outside of the
cell, and the hydrophobic fatty acid chains are buried in the center of the
membrane
Steroids:
Steroids are composed of 4 fused carbon
rings plus some variable
functional side group
-
Cholesterol is a precursor form
of steroid that is modified to produce several other types of steroids
- Cholesterol is a structural
component of the plasma membrane
in animals
- Steroids function as hormones in animal cells
-
Accumulation of large amounts of these bulky molecules in animals can
lead to reduced blood flow and hypertension (high blood pressure)
Proteins:
Proteins are composed of chains of amino acid monomers
- There are 20+ different amino acids in cells of living organisms
- Amino acids have a basic
core structure plus an additional
functional side chain
-
Each amino acid has a central carbon bonded to an amino group, a carboxylic acid group, a hydrogen atom, and the remaining side chain (R group); it is the R group that differs in different amino
acids
-
Condensation of two amino acids in a growing polypeptide chain
results in the formation of a peptide bond; the peptide bond
joins the amino group of one amino acid to the carboxylic acid of the previous
amino acid in the polypeptideŠ the R groups do not normally bond between amino
acids (the exception is cysteine,
which forms disulfide (S-S) bonds within and between polypeptide chains for added strength
Proteins:
-
Hydrolysis of peptide bonds
occurs between specific amino acids in a protein by the activity of specific
enzymes (e.g.: pepsin)
-
R groups can be nonpolar
& hydrophobic, or polar & hydrophilic, depending on the atoms present
Polypeptide:
a chain of many amino acids
joined by peptide bonds
- a protein can be composed of one or several polypeptide chains
Protein
Structure
Primary
Structure: the sequence of amino acids in a polypeptide chain
Secondary
Structure: the formation of discrete structures involving several amino
acids within a polypeptide chain (held together by hydrogen bonds)
a. Alpha
helices