Chemical Foundations for Cells

Chapter 6

Chemical Benefits and Costs

• Understanding of chemistry provides fertilizers, medicines, etc.

• Chemical pollutants damage ecosystems

Elements• Fundamental forms

of matter

• Can’t be broken

apart by normal

means

• 92 occur naturally

on Earth

Most Common Elements in Living Organisms

Oxygen = 65%

Hydrogen = 9.5%

Carbon = 18.5%

Nitrogen = 3.3%

What Are Atoms?

• Smallest particles that retain properties

of an element

• Made up of subatomic particles:

– Protons (+)

– Electrons (-)

– Neutrons (no charge)

HYDROGEN HELIUM

electron

proton

neutron

Hydrogen and Helium Atoms

Atomic Number

• Number of protons

• All atoms of an element have the same atomic number

• Atomic number of hydrogen = 1

• Atomic number of carbon = 6

Mass Number

Number of protons

+Number of neutrons

Isotopes vary in mass number

Isotopes

• Atoms of an element with different numbers of neutrons (different mass numbers)

• Carbon 12 has 6 protons, 6 neutrons

• Carbon 14 has 6 protons, 8 neutrons

What Determines Whether Atoms Will Interact?

The number and arrangement of their electrons

Atoms seek to be more stable – complete orbitals

Electrons

• Carry a negative charge

• Repel one another

• Are attracted to protons in the nucleus

• Move in orbitals - volumes of space that surround the nucleus

Z

X

When all p orbitals are full

y

Electron Orbitals

• Orbitals can hold up to two electrons

• Atoms differ in the number of occupied orbitals

• Orbitals closest to nucleus are lower energy and are filled first

Shell Model

• First shell

– Lowest energy

– Holds 1 orbital with up

to 2 electrons

• Second shell

– 4 orbitals hold up to 8

electrons

CALCIUM20p+ , 20e-

Electron Vacancies

• Unfilled shells make atoms likely to react

• Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells

CARBON6p+ , 6e-

NITROGEN7p+ , 7e-

HYDROGEN1p+ , 1e-

Chemical Bonds, Molecules, & Compounds

• Bond is union between electron structures of atoms

• Atoms bond to form molecules

• Molecules may contain atoms of only one element - O2

• Molecules of compounds contain more than one element - H2O

Chemical Bookkeeping

• Use symbols for elements when writing formulas

• Formula for glucose is C6H12O6

– 6 carbon atoms

– 12 hydrogen atoms

– 6 oxygen atoms

Chemical Bookkeeping

• Chemical equation shows reaction

Reactants ---> Products

• Equation for photosynthesis:

6CO2 + 6H2O ---> + C6H12O12 + 6H2O

Important Bonds in Biological Molecules

Ionic Bonds

Covalent Bonds

Hydrogen Bonds

Covalent Bonding

Atoms share a pair or pairs of electrons to fill outermost shell

•Single covalent bond

•Double covalent bond

•Triple covalent bond

Nonpolar Covalent Bonds

• Atoms share electrons equally

• Nuclei of atoms have same number of protons

• Example: Hydrogen gas (H-H)

Polar Covalent Bonds

• Number of protons in nuclei of participating atoms is NOT equal

• Electrons spend more time near nucleus with most protons

• Water - Electrons more attracted to O nucleus than to H nuclei

Ion Formation

• Atom has equal number of electrons and protons - no net charge

• Atom loses electron(s), becomes positively charged ion

• Atom gains electron(s), becomes negatively charged ion

Ionic Bonding

• One atom loses electrons, becomes positively charged ion

• Another atom gains these electrons, becomes negatively charged ion

• Charge difference attracts the two ions to each other

Formation of NaCl

• Sodium atom (Na) – Outer shell has one electron

• Chlorine atom (Cl) – Outer shell has seven electrons

• Na transfers electron to Cl forming Na+ and Cl-

• Ions remain together as NaCl

7mm

SODIUMATOM11 p+

11 e-

SODIUMION

11 p+

10 e-

electron transfer

CHLORINEATOM17 p+

17 e-

CHLORINEION

17 p+

18 e-

Fig. 2.10a, p. 26

Formation of NaCl

Hydrogen Bonding

• Molecule held together by polar covalent bonds has no NET charge

• However, atoms of the molecule carry different charges

• Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule

onelargemolecule

anotherlargemolecule

a largemoleculetwistedbackonitself Fig. 2.12, p. 27

Examples of Hydrogen Bonds

Hydrogen Ions: H+

• Unbound protons

• Have important biological effects

• Form when water ionizes

The pH Scale

• Measures H+ concentration of fluid• Change of 1 on scale means 10X

change in H+ concentration

Highest H+ Lowest H+

0---------------------7-------------------14Acidic Neutral Basic

Acids & Bases

• Acids

– Donate H+ when dissolved in water

– Acidic solutions have pH < 7

• Bases

– Accept H+ when dissolved in water

– Acidic solutions have pH > 7

Properties of Water

Polarity

Temperature-Stabilizing

Cohesive

Solvent

Water Is a Polar Covalent Molecule

• Molecule has no net charge

• Oxygen end has a slight negative charge

• Hydrogen end has a slight positive charge

O

H H

O

H

HO

H

H

+ _

++

+

_

+

+

Liquid Water

Water Cohesion• Hydrogen bonding holds

molecules in liquid water together

• Creates surface tension

• Allows water to move as continuous column upward through stems of plants

Temperature-Stabilizing Effects

• Liquid water can absorb much heat before its temperature rises

• Why?

• Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules

Why Ice Floats

• In ice, hydrogen bonds lock molecules in a lattice

• Water molecules in lattice are spaced farther apart then those in liquid water

• Ice is less dense than water

Water Is a Good Solvent

• Ions and polar molecules dissolve easily in water

• When solute dissolves, water molecules cluster around its ions or molecules and keep them separated

Spheres of Hydration

Diffusion

• Brownian motion – molecules are in constant motion

• Diffusion – movement from area of high concentration to area of low concentration– Affected by

• Concentration• Temperature or agitation• Pressure

Dynamic Equilibrium

• Molecules are still in motion

• No net gain or loss of molecules

• Living systems seek to achieve

Organic Compounds

Hydrogen and other elements covalently bonded to carbon

Carbohydrates

Lipids

Proteins

Nucleic Acids

Carbon’s Bonding Behavior

• Outer shell of carbon has 4 electrons; can hold 8

• Each carbon atom can form covalent bonds with up to four atoms

Bonding Arrangements

• Carbon atoms can form chains or rings

• Other atoms project from the carbon backbone

Condensation Reactions

• Form polymers from subunits

• Enzymes remove -OH from one molecule, H from another, form bond between two molecules

• Discarded atoms can join to form water

Fig. 3.4a, p. 37

enzyme action at functional groups

CONDENSATION

Hydrolysis

• A type of cleavage reaction

• Breaks polymers into smaller units

• Enzymes split molecules into two or more parts

• An -OH group and an H atom derived from water are attached at exposed sites

enzyme action at functional groups

HYDROLYSIS

Fig. 3.4b, p. 37

Carbohydrates – energy source

Monosaccharides

(simple sugars)

Disaccharides

(two simple sugars)

Polysaccharides

(complex carbohydrates)

Monosaccharides

• Simplest carbohydrates

• Most are sweet tasting, water soluble

• Most have 5- or 6-carbon backbone

Glucose (6 C) Fructose (6 C)

Ribose (5 C) Deoxyribose (5 C)

Two Monosaccharides

glucose fructose

Disaccharides

• Two monosaccharides covalently bonded

• Formed by condensation reaction

+ H2O

glucose fructose

sucrose

Polysaccharides

• Straight or branched chains of many saccharides

• Most common are composed entirely of glucose– Cellulose

• tough, indigestible

• structural material in plants

– Starch• easily digested

• storage form in plants

– Glycogen• sugar storage form in animals

– Chitin• structural material for hard parts of invertebrates

• cell walls of many fungi

• Most include fatty acids– Fats– Phospholipids– Waxes

• Tend to be insoluble in water

• Energy source, insulation & protection

Lipids

Fatty Acids

• Carboxyl group (-COOH) at one end

• Carbon backbone (up to 36 C atoms)

– Saturated - Single bonds between carbons

– Unsaturated - One or more double bonds

Three Fatty AcidsWhat difference does the double bond make?

stearic acid oleic acid linolenic acid

Fats

• Fatty acid(s)

attached to

glycerol

• Triglycerides are

most common

Proteins

• Carbon, hydrogen, oxygen, nitrogen & sulfur

• Amino acid building blocks

• AA linked by peptide bonds

• Enzymes

• Build tissue

Enzymes

• Protein

• Act as catalyst– Helps reaction happen faster or at lower

temperatures

• Substrate specific shapes– Lock & key system– Recycled; not used up

Denaturation• Disruption of three-

dimensional shape

• Breakage of weak bonds

• Causes of denaturation:– pH

– Temperature

• Destroying protein shape disrupts function

Nucleic Acids

• Carbon, hydrogen, oxygen, nitrogen & phosphorus

• Nucleotides – building blocks

• DNA, RNA

• Genetic information