AP Biology 2007-2008

UNIT 1BIOCHEMISTRYPart 1

Hillis Textbook Chapter 2

Chemistry of Life

AP Biology

Living and nonliving matter is composed of atoms.

Like charges repel; different charges attract.

Most atoms are neutral because the number of electrons equals the number of protons.

The number of protons identifies an element.•Number of protons = atomic number

•Atomic Mass or Weight= total number of protons and neutrons

Octet rule—atoms with at least two electron shells form stable molecules so they have eight electrons in their outermost

shells. Valence electrons are the outermost electrons.

AP Biology

Element—pure substance that contains only one kind of atom

Living things are mostly composed of 6 elements:

Carbon (C) Hydrogen (H) Nitrogen (N)

Oxygen (O) Phosphorus (P) Sulfur (S)

AP Biology

Behavior of electrons determines whether a chemical bond will form and what shape the bond will have.

Atoms with unfilled outer shells tend to undergo chemical

reactions to fill their outer shells.

They can attain stability by sharing electrons with other atoms or by losing

or gaining electrons.

The atoms are then bonded together into molecules.

AP Biology

A chemical bond is an attractive force that links atoms together to form molecules. There are several kinds of chemical bonds.

AP Biology

Ions are charged particle that form when an atom gains or loses one or more electrons.

Cations—positively charged ions

Anions—negatively charged ions

Ionic bonds result from the electrical attraction between ions with opposite charges.

The resulting molecules are called salts.

IONIC BONDS

AP Biology

Ionic attractions are weak, so salts dissolve easily in water.

AP Biology

Covalent bonds form when two atoms share pairs of electrons.

The atoms attain stability by having full outer shells.

Each atom contributes one member of the electron pair.

Carbon atoms have four electrons in the outer shell—they can form covalent bonds with four other atoms.

COVALENT BONDS

AP Biology

AP Biology

Properties of molecules are influenced by characteristics of the covalent bonds:

Orientation—length, angle, and direction of bonds between any two elements are always the same.

Example: Methane always forms a tetrahedron.

Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.

Multiple bonds

Single—sharing 1 pair of electrons

Double—sharing 2 pairs of electrons

Triple—sharing 3 pairs of electrons

C C

N N

C H

AP Biology

Attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule forms hydrogen bonds.

They form between water molecules. They are important in the structure of DNA and

proteins.

HYDROGEN BONDS

AP Biology

Water molecules form multiple hydrogen bonds with each other—this contributes to high heat capacity.

A lot of heat is required to raise the temperature

of water—the heat energy breaks the hydrogen bonds.

In organisms, presence of water shields them

from fluctuations in environmental temperature.

WATER!

AP Biology

Water has a high heat of vaporization—a lot of heat is required to change water from liquid to gaseous state. Thus, evaporation has a cooling effect on the environment.

• Sweating cools the body—as sweat evaporates from the skin, it transforms some of the adjacent body heat.

Hydrogen bonds also give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension.

• This permits narrow columns of water to move from roots to leaves of plants.

AP Biology

Any polar molecule can interact with any other polar molecule through hydrogen bonds. WATER IS POLAR!

Hydrophilic (“water-loving”)—in aqueous solutions, polar molecules become separated and surrounded by water molecules

Nonpolar molecules are called hydrophobic (“water-hating”); the interactions between them are hydrophobic interactions.

AP Biology

Why study Carbon? All of life is built on carbon Cells

~72% H2O ;) ~25% carbon compounds

carbohydrates lipids proteins nucleic acids

~3% salts Na, Cl, K…

AP Biology

Chemistry of Life Organic chemistry is the study of

carbon compounds C atoms are versatile building blocks

bonding properties 4 stable covalent bonds

HHC

H

H

AP Biology

Hydrocarbons Combinations of C & H

non-polar not soluble in H2O

hydrophobicstablevery little attraction

between molecules a gas at room temperature

methane(simplest HC)

AP Biology

Hydrocarbons can grow

AP Biology

Isomers Molecules with same molecular formula

but different structures (shapes) different chemical properties different biological functions

6 carbons

6 carbons

6 carbons

AP Biology

Form affects function Structural differences create important

functional significance amino acid alanine

L-alanine used in proteins but not D-alanine

medicines L-version active but not D-version

sometimes withtragic results…

stereoisomersstereoisomers

AP Biology

Form affects function Thalidomide

prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects

AP Biology

Diversity of molecules

Substitute other atoms or groups around the carbon ethane vs. ethanol

H replaced by an hydroxyl group (–OH)

nonpolar vs. polar

gas vs. liquid

biological effects!

ethane (C2H6) ethanol (C2H5OH)

AP Biology

Functional groups Parts of organic molecules that are

involved in chemical reactions give organic molecules distinctive

properties hydroxyl amino

carbonyl sulfhydryl

carboxyl phosphate

Affect reactivity makes hydrocarbons hydrophilic increase solubility in water

AP Biology

Viva la difference! Basic structure of male & female

hormones is identical identical carbon skeleton attachment of different functional groups interact with different targets in the body

different effects

AP Biology

Hydroxyl –OH

organic compounds with OH = alcohols names typically end in -ol

ethanol

AP Biology

Carbonyl C=O

O double bonded to C if C=O at end molecule = aldehyde

if C=O in middle of molecule = ketone

AP Biology

Carboxyl –COOH

C double bonded to O & single bonded to OH group compounds with COOH = acids

fatty acidsamino acids

AP Biology

Amino -NH2

N attached to 2 H compounds with NH2 = amines

amino acids

NH2 acts as base

ammonia picks up H+ from solution

AP Biology

Sulfhydryl –SH

S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins

AP Biology

Phosphate –PO4

P bound to 4 O

connects to C through an O

lots of O = lots of negative chargehighly reactive

transfers energy between organic molecules ATP, GTP, etc.