AP Biology

Textbook Notes Ch. 3 -5

Chapter 3
- Life evolved in water for 3 bill. years before entering land
- Cells are 70-95% water & of Earths surface is water
- Water is the only common substance to exist in environment in all 3 states
- Bonds holding hydrogens to oxygen are POLAR COVALENT b/c Oxy. is more
electronegative than hydo. and so oxy has partial neg. charg. and hydro has partial pos.
- Waters 4 attributes that contribute to life:
1. Cohesive
2. Moderates temperature
3. Expands when freezing
4. Good solvent
- Frequent and brief hydrogen bonds cause cohesion.
- In plants, H-bond helps transport water and nutrients despite gravity
- As water evaporates in leaves, H-bond pulls the liquid water up with it, extending all the
way to the bottom of the tree w/ aid of water-conducting cells
- Also adhesion to cell walls counters gravity
- Also surface tension allows animals and insects to walk and run on water
- Water can absorb massive amounts of heat without changing its temp.
- Heat is TOTAL amount of kinetic energy due to molecular movement. Temperature is
intensity of heat due to average kinetic energy. (e.g. human body has less heat than lake,
but higher temperature)
- 1 calorie = 4.184 Joules
- Specific heat is amount of heat it takes to raise 1 gram of substance 1 degree Celsius
- Water has high SH because most of heat energy is used to break hydrogen bonds before
temp. can increase
- Water warms the air at night in tropical regions by releasing all that stored heat
- Water has high heat of vaporization takes much energy to evaporate
- Ice is less dense than liquid b/c of H-bond. Highest density of water is at 4 degrees C
- Sphere of H2O around dissolved ion is called Hydration Shell
 - Water adheres to cellulose fibers
- 1 mol = 6.022 x 1023
- Molarity (M) : moles of solute per L of solvent
- H2O H+ + OH-
- 10-7 M concentration of H+ or OH- ions in water at 25 degrees C. It cancels out
- Acids increase concentration of H+ when it disassociates (ex. HCl H+ + Cl- )
- Bases reduce concentration of H+ either by binding to them or increasing OH-
- HCl is a strong acid because it reacts completely (no double arrow)
- @ 25o C, [H+] [OH-] = 10-14 M always
- pH = log[H+]
- cells contain buffers to minimize changes in pH by accepting H+ ions in excess and
donating H+ when depleted (e.g H2CO3 HCO3- + H+ )
- normal rain has pH of 5.6 b/c of naturally occurring carbonic acid but acid rain is more
acidic usually b/c of sulfur oxides and nitrogen oxides from pollution

Chapter 4
- molecules containing carbon = organic
- major elements of life: C, H, O, N, S, and P
- vitalism belief in life force (original belief before evolution took over)
- mechanism view that all life governed by physiochemical laws
- carbon tends to form tetrahedrons
- CO2 sometimes considered inorganic b/c no Hydrogen
- Hydrocarbons organic molecules consisting of only carbon and hydrogen
- Hydrocarbons not prevalent in living organisms
- H-carbs are non-polar so hydrophobic & they release large amounts of energy (found in
fats and petroleum)
- Isomers same molecules and same formula, just different organizations
- Structural Isomers differ in arrangement of covalent bonds and location of double
bonds
 - Geometric Isomers differ in arrangement about a double bond (double bond relationship
maintains because it is inflexible) They are distinguished by parallel or diagonal
variations called cis isomer and trans isomer respectively.
- Enantiomers differ in spatial arrangement around an asymmetric carbon (a carbon
attached to 4 different atoms, or clusters of atoms). They are distinguished by left and
right arrangements called L isomer and D isomer respectively.
- Usually 1 enantiomer is biologically active and the other is not. One can even be harmful
while the other is helpful.
- Functional groups components of organic molecules most commonly involved in
reactions
- 6 most important functional groups:
1. Hydroxyl (OH)
2. Carbonyl (CO)
3. Carboxyl (COOH)
4. Amino (NH2)
5. Sulfhydryl (SH)
6. Phosphate groups (OPO32- )

Chapter 5 (5.1)
- Four large biological molecules: carbohydrates, lipids, proteins & nucleic acids
- Carbs, proteins, and N-acids are all polymers (made of monomers)
- Condensation Reaction 2 monomers are connected when they abandon their H & OH
respectively to form water and then covalently bond to each other. This, specifically, is a
dehydration reaction b/c water is lost.
- Reactions must be induced by enzymes
- Hydrolysis breaks polymers apart by adding water and having the OH and H attach
back to the monomers
- All of lifes polymers constructed from only 40-50 available monomers this creates a
vast variety of combinations
5.2
- Carbohydrates include sugars (monosaccharides (simplest), disaccharides,
polysaccharides)
- Monosaccharides are usually multiples of CH2O (ex. Glucose C6H12O6)
- Trademark of sugar = 1 carbonyl group, many hydroxyl groups
- Depending on the location of the carbonyl group, a sugar is either an aldose (aldehyde
sugar) or a ketose (ketone sugar)
- Glucose is aldose; fructose (structural isomer of glucose) is ketose
- Sugars with 6 carbons hectoses; sugars w/ 3 carbons trioses; sugars w/ 5 carbons
pentoses.
- In aqueous solutions, sugars form rings, not chains
- Sugars used for energy, amino & fatty acid construction, or inc. into disacchs. Or
polysacchs.
- 2 monosaccharides formed by glycosidic linkage (covalent bond formed by dehydration
reaction) = disaccharide
- Polysaccharides can serve as storage, to be hydrolyzed when sugar is needed or structures
to protect the cells
- Starch is a storage polysaccharide of plants, consists entirely of glucose monomers
- Plants store starch as granules in structures called plastids (which includes chloroplasts)
- Animals store glycogen for energy in liver and muscle cells
- Polysaccharide cellulose is major component in plant cell walls & the most abundant
organic compound on Earth
- Cellulose, like starch, is a polymer of glucose, except that glycosidic linkages differ
based on the fact that glucose has 2 different ring structures, one in which (OH) attached
to carbon 1 is above () and one below ()
- Starch uses config. but cellulose uses config. So starch is helical but cellulose is
straight
- In plant cell walls, parallel cellulose chains are grouped into microfibrils
- Enzymes that digest starch cannot hydrolyze cellulose (b/c of shapes)
- Some bacteria can break down cellulose to glucose
- Chitin is another polysaccharides used in insect exoskeletons
5.3
- Lipids do not have polymers
- Lipids consist mostly of non-polar hydrocarbons, are hydrophobic
- Examples include fats, phospholipids and steroids.
- Fat is constructer from glycerol and fatty acids
- In making a fat, three fatty acid molecules each join to glycerol by an ester linkage ( a
bond between a hydroxyl group and a carboxyl group)
- Basic unit of fat is then triacylglycerol, (1 glycerol + 3 fatty acids)
- If there are no double bonds b/w carbons of fatty acid, then maximal amount of
hydrogens can bond to the acid hence saturated fat (saturated w/ hydrogen)
- Unsaturated fats have a kink in their geometry wherever cis double bonds occur,
preventing them from compacting close enough to solidify
- Hydrogenated oils are unsaturated fats that have been synthetically saturated with
Hydrogen
- Hydrogenation also produces unsaturated fats w/ trans double bonds called trans fats
- A gram of fat stores twice as much energy as gram of polysaccharide
- Humans and other mammals stock their long-term food reserves in adipose cells, which
swell and shrink as fat is deposited and withdrawn from storage
- Adipose tissue cushions organs and insulates the body
- Phospholipids have only 2 (nonpolar) fatty acids & 1 (polar) phosphate group attached to
glycerol
- Additional charged molecules link to phosphate group to form variety of phospholipids
- Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
- Cholesterol is a steroid in cell membranes & also helps synthesize other steroids
- Many hormones are steroid produced from cholesterol

5.4
- Enzymes are most common proteins - catalyze reactions without being consumed
- Proteins are all constructed from same set of 20 amino acids
- Polypeptides = polymers of amino acids
- 1 or more polypeptides folded into specific geometries constitute proteins
 - Amino acids have amino and carboxyl groups joined to an asymmetric carbon carbon
- The carbon has amino & carboxyl group, hydrogen atom, and variable R group (or side
chain)
- Negatively charged side chains are acidic, positive are basic
- 2 amino acids bond when amino group of one reacts with carboxyl group of the other via
enzymatically catalyzed dehydration reaction.
- ^^^^^^creating a peptide bond
- Many peptide bonds form polypeptide with a C-terminus (carboxyl end) and N-
terminus (Amino end)
- The continuous sequence of the same molecular structure after all the peptide bonds have
been formed is called the peptide backbone
- Frederick Sanger studied insulin
- Protein isnt just polypeptide, but polypeptide(s) conformed into a specific shape
- Polypeptides fold spontaneously via bonds between parts of itself
- Proteins structure divided into: primary, secondary, tertiary, and quaternary
- Denaturation factors such as temperature, pH, and salt concentration of environment
alter the shape of a synthesized protein & makes it biologically inactive
1. When protein moved from aqueous envir. to organic solvent & hydrophobic
regions fold out
2. Chemicals disrupt hydrogen, ionic, and disulfide bridges that maintain protein
shape
3. Excessive heat could agitate polypeptide chain enough to break weak bonds
- Chaperonins - protein molecules that assist the proper folding of other proteins
- X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy aid in
determining protein geometry

5.5
- Each chromosome consists of 1 long DNA molecule that contains hundreds of genes
- One gene on DNA sequence directs the synthesis of mRNA
- Ribosomes are the sites of protein synthesis where the mRNA docks and releases info
- Even prokaryotes (which lack nuclei) use RNA
- Nucleic acids are macromolecules that exist as polymers called polynucleotides
- Each nucleotide is composed of: Nitrogenous base, pentose, and phosphate
- The portion of the group without the phosphate is called nucleoside
- 2 types of nitrogenous bases: Purines & Pyrimidines
- Pyrimidine has 6 membered ring of carbon and nitrogen atoms (which take up H+ from
solution, hence base)
- Cytosine, Thymine, and Uracil are all Pyrimidines
- Purines are larger, with a six-membered ring fused to a five-membered ring (Adenine
and Guanine)
- Thymine is only in DNA & Uracil is only in RNA, rest are in both
- The pentose connected to the nitrogenous base is ribose in the nucleotides of RNA and
deoxyribose in DNA
- We use symbol (prime) to distinguish carbons on the pentose from those on n-base
- Adjacent nucleotides are joined by covalent bonds called phosphodiester linkages
- DNA strand has a built-in directionality along its sugar-phosphate backbone, from 5 to
3
- For DNA, the two sugar-phosphate backbones run in opposite 5 3 directions from
each other, an arrangement referred to as antiparallel
- Both strands held together by hydrogen bonds