---- AP Bio Notes

3.1-3.4 (pg 40-50)


------------------------
key terms:
Macromolecules
Emergent Properties
Valence
Carbon Skeletons
Hydrocarbons
ATP vs ADP
Polymers, Monomers
Enzymes
Dehydration Reaction
Hydrolysis
Glycosidic Linkage
Structural polysacchrides
starch - alpha
cellose - beta
microfibrils
Chitin
----------------------------


Carbon Compounds and Life
‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾

Overview:


Water = universal medium of life

Hydrogen, Nitrogen, Oxygen, Sulfur, and Phosphorus ‾
	accounts for majority of biological materials

All important large molecules fall into 4 categories:
	Carbohydrates, Lipids, Protiens, and nucleic acids

Carbohydrates, protiens, nucleic acids : HUGE
	Called Macromolecules
           ‾‾‾‾‾‾‾‾‾‾‾‾‾‾

Macromolecules can have mass of over 100,000 daltons

Has Emergent properties from elements


&3.1: Carbon atoms can form diverse molecules by bonding to four other atoms


The formation of bonds with Carbon:
Carbon has 6 electrons, 4 valence

Forms tetrahedral molecule shape
109.5 degree bond angle

Structured Formula:
O=C=O
CO2
Two double bonds, same # electrons as 4 single bonds

$ Molecular Diversity Arising from Variation in Carbon Skeletons

Carbon skeletons: strings of carbon making 'core' of molecules

Four ways that carbon skeletons can vary:

(a) Length
  H H              H H H
  | |              | | |
H-C-C-H          H-C-C-C-H
  | |              | | |
  H H              H H H

Ethane            Propane

(b) Branching

                    H
                    |
                  H-C-H
  H H H H           |
  | | | |         H | H
H-C-C-C-C-H       | | |
  | | | |       H-C-C-C-H
  H H H H         | | |
                  H H H

Butane         2-Methylpropane (isobutane)

(c) Double Bond Position

  H H H H      H H H H
  | | | |      | | | |
H-C=C-C-C-H  H-C-C=C-C-H
  | | | |      | | | |
  H H H H      H H H H

(d) Presence of Rings

                      H
    H   H             |
     \ /          H   C   H
   H  C  H         \ / \\/
    \/ \/           C   C
  H-C   C-H         ||  |
  H |   | H         C   C
   \C   C/         /\   //\
   / \ / \        H   C   H
  H   C   H

  Cyclohexane        Benzene

Carbon chains form skeletons of most molecules
Carbon skeletons sometimes double bonds - vary location, number
Important in molecular complexity and diversity


$ Chemical Groups Most Important to Life
 ____________________________________________________________________________________________
|Chemical Group         |   Compound Name    |               Examples                        |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
|Hydroxyl Group (-OH)   |      Alcohol       |     Ethanol (H-C-C-OH)                        |
|_______________________|____________________|_______________________________________________|
|Carbonyl Group (-C=O)  |ketone if in carbon |                                               |
|                       |skeleton, aldehyde  | Acetone, Propanal                             |
|                       |if at end           |                                               |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
| Carboxyl Group (-COOH)| carboxylic acid or |                                               |
|                       | organic acid       | Acetic acid (vinegar)                         |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
| Amino Group (-NH₂)    | Amine              | Glycine                                       |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
|Sulfhydryl Group (-SH) | Thiol              |  Cysteine                                     |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
|PhosphateGroup(-OPO₃⁻²)|   Organic Phosphate| Glycerol Phosphate                            |
|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾|
| Methyl Group (-CH₃)   | Methylated Compound| 5-Methyl Cytosine                             |
|_______________________|____________________|_______________________________________________|

$ Chem. groups can contribute to mol. function by affecting shape

true for steriod sex hormone Estradiol and Testosterone
    Differs in attached chem. groups

ATP: Source of energy for cellular Processes
phosphate group - adenosine triphosphate (ATP)

-Organic molecule - adenosine
    attached to string of 3 phosphate groups


   O   O   O
  ||  ||  ||
O-P-O-P-O-P-O---Adenosine
  |   |   |
  O   O   O

One phosphate can be split off from H2O reaction
HOPO₃⁻² abbreviated (4) in book
Phosphate group in molecule abbreviated (P)

ATP - (P) = diphosphate (ADP)
$ ATP stores energy in form of potential to react w/ water (releases energy)
(P) sub i or (P)i = inorganic phosphate

                             H₂O
(P)-(P)-(P) Adenosine (ATP) ----> (P)i + (P)-(P)-Adenosine (ADP) + Energy

&3.2: Macromolecules are polymers, built from monomers

polymer = long molecule consisting of many identical building blocks linked by covalent bonds

repeating units = monomers

monomers can have functions of their own

$ The Synthesis and Breakdown of Polymers
Chemical mechanisms that make or break down polymers = same in all cases
facilitated & speeded up by Enzimes ( spec. macromoluecules )
monomers connected in reaction in which two molecules covalently bonded to eachother
     loss of h2o molecule (removed)
     called Dehydration Reaction

When bond forms between monomers, each contributes part of h2o molecule
One provides Hydroxyl (-OH), one Hydrogen (-H)
Repeated as monomers are added

Polymers dissembled by monomers by Hydrolysis
reverse of dehydration reaction

$ The diversity of Polymers
cell has 1000+ dif. macromolecules
diversity huge, possible variety = limitless

&3.3: Carbohydrates serve as fuel and building material

Carbohydrates = both sugars and polymers of sugars
Simplest = monosaccharides (simple sugars)
Monomers from which more complex carbs constructed
Disaccarides = double sugar, covalent bond
Carbs include also polysaccharides
sugar monomers joined by dehydration rxn

$ Sugars
Monosaccharides have mol. formulas multiple of CH₂O
glucose = most common monosacchide = C₆H₁₂O₆
glucose has trademarks of sugar
carbonyl group, multiple hydroxyl groups
sugar carbon skeleton ranges from 3-7 C long
glucose, fructose, other sugars have 6, called Hexoses
Trioses and Pentoses common as well
-ose = end of most sugar names
glucose molecules + other most 5-6 length molecules form rings

Monosaccharides = major cell nutrient
Cellular respiration = cells extracting energy from glucose
series of reactions
carbon sugar skeleton = raw material for sythesis of mols such as amino acids

Disaccharide = 2 monosacchrides
linked by Glycosidic Linkage (covalent bond formed between 2 monosaccs by dehydration)
other disaccharides = sucrose, lactose, maltose

$ Polysacchrides
macromolecules
hundred to thousand monosacchrides
starch (amylose) and glycogen and cellulose = polymers
starch allows storing of glucose
glucose monomers usually = 1-4 linkages (#1 to #4 carbon)
Amylopectin has 1-6 linkages

Simplest form of starch = unbranched

Animals store Glycogen - glucose polymer extensively branched
stored in liver and muscle cells
glycogen stores deplenished in 1 day w/o eating

$ Structural polysacchrides
organisms build from structural polysaccharides
cellulose = major cell wall component
global plants produce 10¹⁴ kg (100 billion tons) of cellulose per year

Cellose is polymer of glucose w/ 1-4 glycosidic linkages
linkages different
two slightly different ring structures
glucose ring, hydroxyl group on #1 carbon is either above or below ring plane
Called Alpha and Beta
Starch, all glucose monomers = alpha
in cellose, all glucose monomers = beta

differing linkages gives distinct 3d shapes
starch/glycogen - helical
cellulose - straight, never branched

plant cell wall - microfibrils
cable-like
strong building material

Celluose major component of paper and only of cotton

Enzimes digest starch by hydrolyzing its alpha linkages are unable to hydrolize the beta linkages b/c different shape

few organisms can digest celluose

Celluose stimulates intestine walls making mucus
aids in passage of food
cow, termite has prokaryotes and protists in stomaches for cellulose digestion
some fungi also, helping cycle chem elements

Chitin - polysacchride - used by arthropods to build exoskeletons
also in fungi, using for cell walls

siilar to cellulose, but glucose monomer has nitrogen appendage


&3.4- Lipids are a diverse group of hydrophobic molecules

lipids = 1 class of large bio moles not true polymers
not big enough to be macromolecules
lipids grouped together b/c hydrophobic
include wax, some pigments,
may have some polar bonds, mainly hydrocarbon regions
will focus on fats, phospholipids, steroids


$ Fats
fats != polymer
large molecule assembled from smaller molecules: Glycerol, Fatty Acids

Glycerol is an alcohol, each of 3 carbons bears hydroxyl group
Fatty acid has long carbon skeleton, usually 16-18 carbons
    carbon at one end in carboxyl (gives name acid)
    rest of skeleton consists of hydrocarbon chains
    c-h bonds in fatty acids makes it hydrophobic
water mols hydrogen bond to eachother, excluding fats

In making fat, 3 fat acid mols joined to glycerol by an Ester Linkage (bond between hydroxyl and carboxyl group)
    called triacylglycerol or triglyceride

saturated fatty acid = no double bonds, saturated w/ hydrogen
unsat fatty acid = 1+ double bonds, each d. bond creates kink in molecule
fat made from sat. fatty acids = sat fat, made from unsat = unsat fat
most animal fats = saturated
hydrocarbon chains of fatty acids ("tails") lack double bonds
flexiblity allows packing tighter

sat. fats = lard, butter
solid at room temp

fats of plants, fishes = unsat in general
usually liquid, called oils
olive oil, cod liver oil example

hydrogenated vegetable oil = unsat fats converted to sat fats by adding oxygen

fats maj. function = energy storage
hydrocarbon in fats similar to gasolene and about as rich in energy

1 g fat has ~2x energy than polysaccharides (starch)
plants immobile - can deal w/ bulky energy storage
animals must move, so use fat

$ Phospholipids
essential for cell membranes

simalar to fat, but w/ 2 fatty acids attached to glycerol, not 3
hydrocarbon tails are hydrophobic, phosphate group and attachments make hydrophilic head

varios small molecules can be linked to phosphate group to form variaty of phospholipids

when phospholipids added to water, form double layered called bilayers, shielding hydrophobic part

$ Steroids
lipids characterized by carbon skeleton w/ 4 fused rings
different steroids distinguished by particular chemical groups attached to rings
cholesterol is crucial steroid
common component of animal cell membranes, also precurser to other steroids, namely estrogen and testosterone
cholesterol is synthesized in liver, obtained from diet
high level cholesterol -> atherosclerosis
sat. fact exert neg. health impact by affecting cholesterol levels.