AP Bio Chapter 4

Organic Chemistry

The study of compounds containing carbon (ex. methane CH4)

Hydrocarbons

Organic molecules consisting of only carbon and hydrogen (hydrophobic and nonpolar)

Isomers

Compounds with the same molecular formula but have different structures resulting in different molecular and chemical properties

How many types of isomers are there?

3: Structural, Geometric, and Enantiomers

Structural Isomers

Different in the covalent arrangements of their atoms (ex. glucose and fructose)

Can functional groups give hydrocarbons different properties?

Yes

Geometric isomers

Has the same covalent partnership but differ in arrangement of atoms; arises from the inflexibility of double bonds

Enantiomers isomers

Molecules that are mirror images of each other usually involving an asymmetric carbon (ex. L Dopa and D Dopa) resulting in organisms being sensitive to even the most subtle variations in molecular architecture the way they attach to cells differ.

Functional Groups

a group of atoms attached to a carbon skeleton and have consistent properties that are given to the molecule

How many functional groups are there?

8: Hydroxyl, Carbonyl, Carboxyl, Amino, Phosphate, Sulfhydryl, (Methyl, and Acetyl = More like forces)

Hydroxyl Group

A hydrogen atom bonded to an oxygen atom; Properties: very polar and is hydrophilic; Can form alcohol; (ex. -OH)

Carbonyl Group

A carbon atom bonded to an oxygen atom by a double bond; Properties: Polar; Forms two types of compounds: Aldehydes and Ketones; (ex. -C=O)

Where is the Aldehyde compound found in the Carbonyl Group?

It's found in the end of a carbon skeleton (ex. R-C=O)

Where is the Ketones compound found in the Carbonyl Group?

It's found in the middle of a carbon skeleton (ex. C-C=O-C)

Carboxyl Group

Carbon double bonded to an oxygen and to a hydroxyl group; donates H+ acid; forms many weak organic acids (ex. -COOH) also called Carboxylic Acids

Amino Groups

Nitrogen bonded to two hydrogens; forms compounds called amines (acts as bases) (ex. H-N-H)

Sulfhydryl Group

Sulfur bonded to a hydrogen; forms compounds called thiols which helps with protein structure and disulfide bridges in DNA and RNA; (ex. -SH)

Phosphate Group

A central phosphorous atom with a net charge of -2; involved with energy transfers like ATP; weak organic acid; (ex. -PO4)

ATP

Energy carrying molecule

Inorganic

When it is not attached to a carbon skeleton

Methyl

-CH3

Nonpolar

Hydrocarbon

Silences DNA expression

Methylation

What is Methylation?

When methyl groups get added

Acetyl

-COCH3

Polar

Copes DNA expression

Acetylation

What is Acetylation

When acetyl groups get added

Chemical Cycling

How matter is recycled through ecosystems observed by studying biogeochemical cycles

Water Cycle (Hydrologic)

Driven by the Sun; Living Components: trees; 3 Steps: Evaporation, condensation, and precipitation; Reservoir: Oceans; Importance: HELPS CYCLE OTHER TYPES OF MATTER (OTHER CYCLES)

Carbon Cycle

Driven by photosynthesis, energy flow, respiration; Living Components: All life (ex. cows, trees, algae, grass); Reservoir: CO2 in the atmosphere= by-product of respiration and the burning of fossil fuels/soil; Importance: Source of fuel and energy to support food chains

Nitrogen Cycle

Driven by Nitrogen Fixation; Living Components: Bacteria; 4 Steps: Decompose/Nitrogen Fixation, Ammonification (Ammonia), Nitrification (Nitrates), Assimilation/Denification; Reservoir: Atomospheric N2/Gas; Importance: Production of: Nucleic acids, Atpm Amino acids

Amino Acids

Proteins

Most abundant gas in the atmosphere

Nitrogen

Phosphorous Cycle (Rock Cycle)

Driven by weather; Living Components: Plants; Reservoir: Sedimentary Rock; Importance: used to make DNA, ATP, phospholipid bilayer of cell membrances (Boundaries aronadour cells)

Why Carbon?

Can form 4 covalent bonds, tetravalence, normally bonds with CHON (Carbon, Hydrogen, Oxygen, and Nitrogen)

What elements are CHON?

Carbon, Hydrogen, Oxygen, Nitrogen

How do you find the molecular weight of each atom?

of Atoms x Atomic Mass = I mole

pH

Power/Potential of Hydrogen measuring the [H+]

What is the bond with a electronegativity of 0-0.5

Non-Polar Covalent

What is the bond with a electronegativity of 0.5-1.7

Polar Covalent

What is the bond with a electronegativity of >1.7

Ionic

Mass of Nucleus

of Protons + # of Neutrons

Acidic

Lower than a pH of 7, has more H+, [H+ x 10]

Basic

Higher than a pH of 7, has more [OH-], [H+ x 1/10]

Which has more H+ (basic or acid)?

Acid

Which has more OH- (basic or acid)?

Basic

cis isomer

the two Xs are on the same side

trans isomer

the two Xs are on opposite sides

Ionized

has become an electrically charged atom or molecule by gaining or losing electrons