Biology Notes. Chapter Three.

Amelia Royce
I. the polarity of water molecules results in hydrogen bonding.
a. polar molecule- opposite ends, opposite charges.
i. hydrogen (-) and oxygen (+)
II. four emergent properties of water contribute to Earth’s fitness for life
a. cohesion and Adhesion
i. hydrogen bonds that hold substance together (cohesion)
ii. water clings to other substances (adhesion)
b. moderation of temperature
i. heat and temperature
I. kinetic energy (motion) measured by heat, intensity of heat due to average kinetic energy
measured by temperature
II. blah, blah, blah measuring.
ii. high specific heat
I. amount of heat to raise 1g by 1 degree
iii. heat of vaporization
I. heat to have 1g become…
a. gaseous
c. solid is less dense than liquid
i. ice floats
d. solvent of life
i. great dissolving agent
 ii. aqueous solution
iii. hydrophilic
I. “water loving”
iv. hydrophobic
I. “water fearing”
v. solute concentration in aqueous solutions
I. sum of masses of atoms (molecular mass)
II. mole
a. molarity- moles of solute/liter solution
III. dissociation of water molecules leads to acidic and basic conditions and affect living
organisms
a. water constantly shifting forms
b. pH and whatnot
i. acid
I. substance that increases the hydrogen ion concentration of a solution
ii. base
I. reduces hydrogen ion concentration
iii. the pH scale
I. 7 is neutral
II. above 7 is basic
III. under 7 is acidic
IV. base 10
iv. buffers
I. substances that minimize changes in pH
v. acid rain
I. pH lower than 5.6
II. pollution and natural causes
III. serious environmental ramifications
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Biology Notes. Chapter Four. Amelia Royce
I. organic chemistry is the study of carbon compounds
I. organic compounds were once thought to only arise in living organisms (vitalism)
i. disproved when chemists were able o synthesize these organic compounds
II. carbon atoms can form diverse molecules by bonding to four other atoms
I. formation of carbon bonds
i. covalent bonding capacity of four
1. diverse molecules
2. bonds with variety of molecules (including O, H, & N)
3. bond to other carbons to form the carbon skeletons of organic
compounds
II. molecular diversity arising from carbon skeleton variation
i. carbon skeletons vary in length and shape
ii. have bonding “sites” for atoms of other elements
iii. hydrocarbons- carbon and hydrogen only
iv. isomers- molecules with same formula but different structures and properties
1. structural
2. geometric
3. enantiomers
III. functional groups most important in chemistry of life
I. chemically reactive groups of atoms within organic molecule
i. give distinctive properties
ii. hydroxyl
 1. –OH
2. polar
3. helps dissolve in water
iii. carbonyl
1. >CO
2. end of carbon skeleton (aldehyde)
a. OR
3. within skeleton (ketone)
iv. carboxyl
1. –COOH
2. found in carboxylic acids
3. hydrogen can dissociate
v. amino group
1. can accept proton making it a base
vi. sulfhydryl group
1. helps stabilize structure of some proteins
vii. phosphate group
1. important role in transfer of energy
IV. ATP- an important source of energy for cellular process
I. phosphate group splits from ATP and is used for energy in the cell

II.
Biology Notes. Chapter Five. 09/08/2010
I. most macro molecules are polymers, built from monomers
 a. synthesis and breakdown of polymers
i. carbs, lipids, proteins, and nucleic acids
1. major organic compound classes
2. many are very large molecules
ii. most macro molecules are polymers (chains of identical or similar monomers)
iii. monomers form larger molecules through condensation reactions (water
released… dehydration)
iv. polymers can disassemble (reverse) hydrolysis
b. diversity of polymers
i. each class formed from specific monomers
ii. unique because of arrangement
iii. immense variety of polymers from little polymers
II. carbohydrates serve as fuel and building material
a. sugars
i. smallest carbohydrates
ii. fuel and carbon sources
iii. simplest- monosaccharides- fuel, converted into other organic molecules, or
combined into polymers
iv. diasaccharides (2) connected by glycosidic linkage
b. polysaccharides
i. polymers of sugars
ii. storage and structure
 iii. monomers connected by glycosidic linkages
iv. starch in plants and glycogen in animals (storage polymers of glucose)
v. cellulose is important structural polymer of glucose in plant cell walls
vi. starch, glycogen, and cellulose differ in positions and orientations of glycosidic
linkages
III. lipids are diverse group of hydrophobic molecules
a. fats
i. store large amounts of energy
ii. triacylglycerols are constructed by joining of glycerol molecule and three fatty
acids by dehydration reactions
1. saturated- max H atoms
2. unsaturated- one or more double bond s in hydrocarbon chains
b. phospholipids
i. major components of cell membrane
ii. two fatty acids, phosphate group, linked to glycerol
iii. head- hydrophilic
iv. tail-hydrophobic
c. steroids
i. cholesterol and certain hormones
ii. four fused rings of carbon atoms
IV. proteins have many structures, resulting in a wide range of functions
a. polypeptides
i. polymer of amino acids in a specific sequence
 ii. protein-one or more polypeptide chains folded in specific 3D formation
iii. 20 amino acids with characteristic side chain
iv. carboxyl group and amino groups of adjacent amino acids link together in
peptide bonds
b. protein conformation and function
i. primary
ii. secondary
iii. tertiary
iv. quaternary
V. nucleic acids store and transmit hereditary information
a. roles of nucleic acids
i. DNA stores information for synthesis of specific proteins
ii. RNA carries this to protein synthesizing machinery
b. Structure of nucleic acids
i. Each nucleotide monomer consists of a pentose covalently bonded to a
phosphate group and to one of four different nitrogenous bases. A, G, C & T or
U. RNA has ribose as its pentose; DNA has deoxyribose. RNA has U; DNA has
T. In a polynucleotide, nucleotides are joined to form a sugar phosphate
backbone from which the nitrogenous bases project. Each polynucleotide strand
has polarity, with a 5 and a 3 end. The sequence of bases along a gene specifies
the amino acid sequence of a particular protein.
c. DNA double helix
i. helical, double stranded macromolecule
ii. bases projecting into the interior of the molecule from two antiparallel
polynucleotide strands
iii. A & T
iv. C & G
v. Nucleotide sequences of 2 strands are complimentary
vi. “copy” one another
VI. tape measures of evolution
a. molecular comparisons help biologists sort out evolutionary connections between
species
On My Test 09/08/2010
 KPCOFGS (Human, Honey Bee, Maple)
 molar solution
 DNA
 RNA
 D or L
 Darwin’s Book/ Natural Selection
 Pure Gangster / Cut Py
 Photosynthesis and Respiration
 Protein structure (thumb question)

Enzyme- lower the activation energy barrier to chemical reaction. Combines with the substrate
in temporary association. Enzyme-substrate complex has lower energy requirement.

The standard free-energy change calculated for AVP varies according to temperature,
concentration, pH, slat content, etc. Although a value of -7.3 kcal for delta G has been calculate
for ATP in some test systems, an average of -7 kcal is often used. Values as high as -12.5 kcal
are believed to be more typical of living cells but undoubtedly delta G varies among cells and
from one time to another.
In a cell the free energy released from the hydrolysis of ATP is used to transfer the phosphate
group to another molecule, producing a phosphorylated molecule that is more reactive (less
stable) THE PHOSPHORYLATION OF OTHER MOLECULES BY ATP FROMS THE BASIS
FOR ALMOST ALL CELLULAR WORK.
Chapter 6 Notes 09/08/2010
I. Eukaryotic cells have internal membranes that compartmentalize their functions
a. Comparing prokaryotic and eukaryotic cells
i. Bounded by plasma membrane
ii. Prokaryotic lack nuclei and other membrane enclosed organelles
b. A panoramic view of the eukaryotic cell
i. Plant and animal cells have mostly similar organelles
II. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by
ribosomes
a. The nucleus: genetic library of cell
i. Houses DNA and nuclei
1. Where ribosomal sub-units are made
ii. Materials pass through pores is nuclear envelope
b. Ribosomes: protein factories in the cell
i. Free ribosomes in cytosol
ii. Bound ribosomes on outside of ER and in nuclear envelope
iii. Both synthesize proteins
III. The endomembrane system regulates protein traffic and performs metabolic functions in the
cell
a. The endoplasmic reticulum: biosynthetic factory
i. Smooth ER
1. synthesizes lipids
2. Metabolizes carbs
3. Stores calcium
 4. Detoxifies poison
ii. Rough ER
1. Poduces proteins
2. And membranes
3. Distributes by transpot vesicles from ER
b. Golgi apparatus: shipping and receiving center
i. From ER to golgi
ii. Modifies, sorted, released to transport
c. Lysosomes: digestive compartments
i. Sacs of hydrolytic enzymes
ii. Break down substances for recycling
d. Vacuoles: divers maintenance compartments
i. Storage, waste disposal, cell growth, protection
IV. Mitochondria and chloroplasts change energy from one form to another
a. Mitochondria
i. Sites of cellular respiration
ii. Outer membrane
iii. Inner membrane folded into cristae
iv. Chloroplasts
b. Chloroplasts
i. Contain pigments that function during photosynthesis
 ii. At least two membranes surround fluid stroma (contains thylakoids stacked into
grana
c. Peroxisomes : oxidation
i. Produce hydrogen peroxide and convert it to water
V. The cytoskeleton is a network of fibers that organizes structures and activities in the cell
a. Roles of cytoskeleton: support, motility, and regulation
i. signal transmission
ii. motility
iii. structural support
b. components of cytoskeleton
i. microtubes shape the cell
1. guide movement of organelles
2. help separate chromosome copies in dividing cells
3. cilia and flagella are motile appendages
4. microfilaments are thin rods built from actin
5.
6. intermediate filaments support shape
c. extracellular components and connections and help coordinate activities
i. cell walls of plants
1. made of cellulose fibers imbedded in other polysaccahrides and
proteins
ii. ECM of animal cells
1. Secrete glycoproteins that form the ECM (support, adhesion,
movement, and regulation)
iii. Intercellular junctions
1. Plasmodesmata that pass through adjoining cell walls
 09/08/2010
“Tree if life”
Different trees are generally similar, but because these exact relationships are still being
debated, the position of roots and limbs may vary. For instance, some genetic genetic evidence
suggests that euks. Evolved from the union of some bacteria and archaea (1 becoming the
nucleus and the other the main cell.

Level of classification above kingdom = domain

Domain Archaea Domain Bacteria Domain Euk,.
Kingdom Archaebacteria Kingdom Eubacterial Remaining four
Halophiles Grams (+)’s Kingdom Protistq
Methanobacteruim Cyanobacteria “ Fungi
“ Plantae
“ Anamalia
Animals Plants
Fungi slime molds

‘kingdom Protista phyla:

Plantlike Protist (photosynthetic)
Euglenphyta, Dinoflagella, chysophyta, chlorophyta, phaeophyta
Chapter 7 Notes 09/08/2010
I. Cellular membranes are fluid mosaics of lipids and proteins
 a. Fluidity of membranes
i. Phospholipids and proteins (to a lesser extent) move laterally within membrane
ii. Cholesterol and unsaturated hydrocarbon tails in the phospholipids affect
membrane fluidity
b. Membrane proteins and their functions
i. Integral proteins are embedded in the lipid bilayer
ii. Peripheral proteins attached to surfaces
iii. functions
I. transport
II. enzymatic activity
III. signal transduction
IV. cell-cell recognition
V. intercellular joining
VI. attachment to cytoskeleton and ECM
c. the role of membrane carbs in cell-cell recognition
i. short chains of sugars linked to proteins and lipids on exterior side of plasma
membrane
ii. interact with surface molecules of other cells
d. synthesis and sidedness f membranes
i. membrane proteins and lipids are synthesized in ER and modifies there and in
Golgi apparatus
ii. inside and outside faces of membrane differ from cell to cell
II. Membrane structures results in selective permeability
 a. A cell must exchange small molecules and ions with surrounding
b. Controlled by plasma membrane
c. The Permeability of the Lipid Bilayer
i. Hydrophobic are soluble
I. Pass through quickly
d. Transport proteins
i. Polar molecules and ions generally require specific ones to help them across
III. Passive transport is diffusion of a substance across a membrane with no energy investment
a. Effects of osmosis on water balance
i. Hypotonic to hypertonic
ii. If isotonic, no net osmosis
iii. Cell survival depends on water balance
iv. Wall- less cells are isotonic with surroundings
IV. Active transport uses energy to move solutes against their gradients
a. The need for energy in active transport
i. Usually use ATP
b. Maintenance of membrane potential by ion pumps
i. Chem.. gradient and voltage, combine to make electrochemical gradient
ii. Determines net direction of ionic diffusion
iii. “pumps” contribute to electro chemical greadients.
V. Bulk transport across the plasma membrane occurs by exocytosis and endocytosis
a. Exocytosis
i. Vesicles migrate to plasma membrane
ii. Fuse and release contents
b. Endocytosis
i. Molecules enter cells with in vesicles
I. Pinch inward from plasma membrane

o
 09/08/2010
I. An organism’s metabolism transforms matter and energy, subject to laws of thermo
dynamics
 a. Organization of chemistry of life into metabolic pathways
i. Metabolism-collection of chem. Reactions that occur in organism
ii. Aided by enzymes
iii. Follows pathways
iv. May be catabolic or anabolic
b. Forms of energy
i. Kinetic, potential, chemical
c. Laws of energy transformation
i. Cannot be created or destroyed; transformed or transferred
ii. Spontaneous change increase entropy of universe
II. Free energy change f reaction tells whether reaction is spontaneous
a. Free energy change ΔG
i. Related to enthalpy change ΔH
ii. And change in entropy (ΔS)
iii. ΔG=ΔH – TΔS
b. Free energy, stability, equilibrium
i. Free energy decrease, stability increase
ii. Equilibrium is max. stability
c. Free energy and metabolism
i. Exergonic products have less than reactants (-ΔG)
 ii. Endergonic require energy input (+ΔG)
iii. Addition of starting materials, removal of ends prevents from reaching
equilibrium
III. ATP powers cellular
a. Structure and hydrolysis of ATP
i. Cell’s energy shuttle
ii. Release of terminal phosphate group produces ADP and phosphate; releases
free energy
b. How ATP performs work
i. drives endergonic reactions by phosphorylation
ii. more reactive… carries out work
IV. Enzymes speed up metabolic reactions by lowering energy barriers
a. Activation energy barrier
i. Energy necessary to break bonds of reactants
b. How enzymes…
i. Speed up reactions, lowering AE barrier
c. Substrate specificity of enzymes
i. Lock and key.
d. Catalysis in enzyme’s active site
i. You know this!
e.
09/08/2010
Chapter 10 10/3/10 5:12 PM

I. Photosynthesis- Light to Food

a. Chloroplasts
i. Site of photosynthesis
ii. In autotrophic eukaryotes
1. Occurs in chloroplasts, containing thylakoids
2. Stacks of thylakoids form grana
b. Tracking Atoms Through Photosynthesis:
i. (insert photosynthesis equation here)
ii. chloroplasts split water into hydrogen and oxygen, incorporating hydrogen
electrons into sugar molecules
iii. “redox process” water is oxidized, carbon dioxide is reduced
c. the two stages of photosynthesis
i. the light reactions in the gran split water releasing dioxide, producing ATP, and
forming NADPH
ii. in the calvin cycle…
1. stroma makes sugar from carbon dioxide, using ATP for energy and
NADPH to reduce power
II. The Light Reactions Convert Solar Energy to the Chemical Energy of ATP and NADPH
a. The nature of sunlight
i. Form of electromagnetic energy
ii. Visible wavelengths include those that drive photosynthesis
b. Photosynthetic Pigments
i. Pigments absorbs visible light of a specific wavelength
ii. Chlorophyll a is the main photosynthetic pigment in plants
 iii. Accessory pigments-absorb other wavelengths in order to pass energy on to
chlorophyll a
c. Excitation of chlorophyll by light
i. Pigment grows from a ground state to an excited state when a photon boost one
of it’s electrons to a higher-energy orbital
ii. Excited state is unstable
iii. Electrons from isolated pigments tend to fall back to ground state, giving of heat
and/or light
d. A Photosystem: A Reaction Center Associated with Light-Harvesting Complexes
i. A Photosystem is composed of a reaction center surrounded by light-harvesting
complexes that funnel energy from photons to reaction center
ii. When a reaction center chlorophyll a molecule absorbs energy one of it’s
electrons gets bumped up to the primary electron adaptor
iii. Photosystem II contains P680
iv. Noncylic electron flow produces
1. NADPH
2. ATP
3. And oxygen
e. Cyclic Electron Flow employs only photosystem 1 producing ATP but no NADPH
or dioxide
f. Chemiosmosis in chloroplasts and mitochondia
i. In both, redox reactions of electron transport chans generate and H positive
gradient across a membrane
ii. ATP synthase uses this protein-motive force to make ATP
III. The Calvin Cycle Uses ATP and NADPH to convert carbon dioxide to sugar
a. Occurs in stroma and consists of carbon fixation, reduction, and regeneration of the
carbon dioxide acceptor
b. Using electrons from NADPH and energy from ATP the cycle synthesizes a G3P
c. Most of G3P is reused
 d. Some exits cycle and is converted to glucose and other organic molecules
IV. Alt. Methods of Carbon Fixation Have Evolved in Hot, Arid Climates
a. Photorespiration: an evolutionary relic?
i. Plants close stomata to conserve water
1. oxygen from light reactions builds up
2. dioxide substitutes for carbon dioxide in active site of rubisco
3. consumes fuel and releases carbon dioxide without producing ATP or
sugar
b. C4 Plants
i. Minimize cost of photorespiration by incorporating carbon dioxide into four-
carbon compounds in mesophyll cells
ii. Exported to bundle-sheath cells where they releas carbon dioxide for use in
Calvin Cycle
c. CAM Plants
i. Open stomata at night incorporating carbon dioxide into organic acids, where
they are stored in mesophyll cells
ii. Closed stomata during day
1. Carbon dioxide released from organic acids for use in Calvin cycle
d. A Review of the Importance of Photosynthesis
i. Organic compounds produced by photosynthesis provide the energy and
building material for ecosystems