CHEMISTRYConcepts and connections

Ch. 2

Atoms, Elements and molecules

• ALL MATTER IS MADE UP OF ATOMS

• ALL MATTER IS ORGANIZED INTO ELEMENTS (in the Periodic Table)

• The fundamental building blocks of life are CHEMICALS

• ELEMENTS: fundamental form of matter that have mass, occupies space and cannot be decomposed into other substance(elements are made up of atoms that are unique for that substance)

Atoms

• ATOM: the smallest unit of an element that still retains the properties of that element

• Living things are composed of about 25 chemical elements.

MOLECULE:• MOLECULE: two or more atoms bonded

together in fixed proportions.

Example: a water molecule. 2 hydrogen atoms bonded with an oxygen atom H2O

• Two molecules : 2H2O

• Cells function and do what they do as a result of chemical reactions

ELEMENTS FOUND IN ALL LIVING

ORGANISMS: • Living organisms contain about 25 chemicals but the four found in ALL

are : CHON (carbon, hydrogen, oxygen and nitrogen)

• These four make up over 96% of our bodies

• Elements found in most life: CHONPS• Others important for life are Mg, Na, K, Cl, Ca, I, Fe• Elements found in very small amounts are “trace

elements” and function as catalysts and co-enzymes• Ex: iodine (I)

• Chemical symbols are universal. C= carbon H= hydrogen O= oxygen • N= nitrogen P=phosphorous S= sulfur Mg= magnesium Na= sodium

K= potassium Ca=calcium Fe= iron

– Carbon, hydrogen, oxygen, and nitrogen • Make up the bulk of living matter

Table 2.1

CONNECTION• Trace elements are common additives to food and water

– Dietary deficiencies in trace elements• Can cause various physiological conditions

Figure 2.2A

ATOMS

• Atoms are made up of:

PROTONS (p+) (positive charge) in the nucleus

NEUTRONS (n) (no charge) in the nucleus

ELECTRONS (e-) (negative charge) in the energy levels around the nucleus

LE 2-8

Firstshell

Hydrogen

1H

Lithium

3Li

Secondshell

Thirdshell

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

12AlSilicon

14Si

Carbon

6CNitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16SChlorine

17Cl

Fluorine

9FNeon

10Ne

Argon

18Ar

Helium

2HeAtomic number

Element symbol

Electron-shelldiagram

Atomic mass

2He4.00

Electron Configuration and Chemical Properties

• The chemical behavior of an atom is determined by the distribution of electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

Atoms are electrically neutral

• The number of protons(+) in the nucleus = the number of electrons(-) around it

# of protons= # of electrons

• Atomic number = the number of protons in the nucleus

• Atomic mass = the number of protons + the number of neutrons added together

Subatomic Particles• Atoms are composed of subatomic particles

• Relevant subatomic particles include:– Neutrons (no electrical charge)– Protons (positive charge)– Electrons (negative charge)

• Neutrons and protons form the atomic nucleus

• Electrons form a cloud around the nucleus

LE 2-4

Nucleus

ElectronsCloud of negativecharge (2 electrons)

• Valence electrons are those in the outermost shell, or valence shell

• The chemical behavior of an atom is mostly determined by the valence electrons

LE 2-7b

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Atomicnucleus

Energyabsorbed

Energylost

ISOTOPES• Isotopes are atoms of a given element that

have the same number of protons and electrons but have a different number of neutrons.

• They have the same atomic number but different mass number.

Ex: Carbon (C) there are 6 protons and 6 electrons in carbon but it can have different # of neutrons such as 12C, 13C, 14C

•Medical Diagnosis– Radioactive tracers are often used for diagnosis

• In combination with sophisticated imaging instruments

Figure 2.5A Figure 2.5B

LE 2-6

Cancerousthroattissue

Uses of Isotopes• In medicine and research as labels and

tracers. For Diagnosis: can take pictures with PET scans and other

devices. we can detect them with scintillating machines and follow their movements

For treatment: we use radium and cobalt to destroy cancerous tumors

• To date ancient objects:Since we know the half life of an element ( time it takes for

half of it to decay to a stable form) we can calculate how long it has been around.

• Electron arrangement determines the chemical properties of an atom

– Electrons in an atom • Are arranged in shells, which may contain

different numbers of electrons

Hydrogen (H)Atomic number = 1

Electron

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

Figure 2.6

– Atoms whose shells are not full • Tend to interact with other atoms and gain,

lose, or share electrons

– These interactions• Form chemical bonds

Chemical bonds in living organisms• The three major chemical bonds used by

elements to build compounds are:

• Ionic bonds

• Covalent bonds

• Hydrogen bonds

IONS• Atoms become IONS or ionized when

they lose or gain electrons so the number of protons is different than the number of electrons.

• When an atom gains electrons it has more –(negative ) charges. It becomes a negative ion

• When it loses electrons now it has more positive charges. It becomes a positive ion

•Ionic bonds are attractions between ions of opposite charge

– When atoms gain or lose electrons• Charged atoms called ions are created

Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ion

Cl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

Figure 2.7A

– An electrical attraction between ions with opposite charges

• Results in an ionic bond

– Sodium and chloride ions • Bond to form sodium chloride, common table salt

Na+

Cl–

Figure 2.7B

•Covalent bonds join atoms into molecules through electron sharing

– In covalent bonds• Two atoms share one or more pairs of outer shell

electrons, forming molecules

• A molecule consists of two or more atoms held together by covalent bonds

• A single covalent bond, or single bond, is the sharing of one pair of valence electrons

• A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

• Covalent bonds can form between atoms of the same element or atoms of different elements

Animation: Covalent BondsAnimation: Covalent Bonds

LE 2-11b

Oxygen (O2)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

– Molecules can be represented in many ways

Table 2.8

• Unequal electron sharing creates polar molecules

– A molecule is nonpolar• When its covalently bonded atoms share

electrons equally

– In a polar covalent bond• Electrons are shared unequally between atoms,

creating a polar molecule(–) (–)

(+) (+)

O

HH

Figure 2.9

•Hydrogen bonds are weak bonds important in the chemistry of life

– The charged regions on water molecules• Are attracted to the oppositely charged

regions on nearby molecules

– This attraction forms weak bonds • Called hydrogen bonds

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

Figure 2.10

WATER

Life began in water and land organisms essentially carry their wet environment inside themselves. Water accounts for 75 to 85% of a cell’s weight, and most cells are surrounded by it.

About 71% of Earth’s surface is covered by oceans and human bodies are about 66% water.

If you weigh 128bl, 85 pounds of you is water.• Water plays a major role in many of life’s

processes.

WATER’S LIFE-SUPPORTING PROPERTIES

• Hydrogen bonds make liquid water cohesive (molecules “stick” to each other)

– Due to hydrogen bonding– Cohesiveness makes water molecules move

from a plant’s roots to its leaves

– Insects can walk on water due to surface tension

• Created by cohesive water molecules

Figure 2.11

• Water’s hydrogen bonds moderate temperature

– Water’s ability to store heat• Moderates body temperature and climate

• Ice is less dense than liquid water– Hydrogen bonds hold molecules in ice

• Farther apart than in liquid water

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogen bondFigure 2.13

– Ice is therefore less dense than liquid water• Which causes it to float

– Floating ice• Prevents lakes and oceans from freezing

solid. The water under the ice remains warmer

• protects the living things beneath the ice

• Water is the solvent of life– Polar or charged solutes dissolve when water

molecules surround them, forming aqueous solutions

+

–

–

–

–

–

–

–

–

––

++

+

++

Na+

+

Na+

Cl–

Ion insolution Salt

crystal

Cl–

Figure 2.14

WATER PROPERTIES

• Water is the best solvent for living things. It can dissolve more substances in greater mounts than any other liquid. Everything that goes In and out of cells is dissolved in H2O

This is because of its polarity and hydrogen bonds. • Water is a polar molecule (slightly negative at the oxygen end

and slightly positive at the hydrogen end). Polar molecules are hydrophilic (water loving)

A hydrophobic substance is one that dislikes water, it is nonpolar .Ex: oils

• Because water forms hydrogen bonds with other water molecules ,they are spaced apart when frozen, so ice is less dense than liquid water and it floats on it.

• Ice on the surface insulates the water beneath it, keeping it warmer.

Water Properties (continued….)• Water has temperature stabilizing effect.

This is because it can absorb a lot of heat before its temperature changes.

Heat increases the molecular motion so much that hydrogen bonds are broken and water molecules escape into the air. This is evaporation, cooling the surface.

• Water’s cohesion creates surface tension. Cohesion is the capacity to resist rupturing. Water “sticks together” as a result of its hydrogen bonds.

• Cohesion is very important for plants to pull water from the soil.

• The chemistry of life is sensitive to acidic and basic conditions

– A compound that releases H+ ions in solution is an acid

• And one that accepts H+ ions in solution is a base

– Acidity is measured on the pH scale • From 0 (most acidic) to 14 (most basic)• Neutral pH is 7

Acids, Bases and Buffers: The pH scale

PH is the measure of the H+ (hydrogen ions) concentration in a solution. The greater the H+ conc. The lower the pH.

• The scale goes from 0( acidic) to 7 (neutral) to 14 (basic)

• What is an acid? A substance that releases hydrogen ions in

solution is an acid. Ex: HCl (hydrochloric acid)

• What is a base? Substances that release OH-(hydroxyl ions) in

solution are called bases and are alkaline.

The pH scale

Basic solution

Oven cleaner

Acidic solution

Neutral solution

pH scale0

1

2

3

4

5

6

7

8

9

10

11

12

Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Incr

easi

ngly

AC

IDIC

(Hig

her

conc

entr

atio

n of

H+)

NEUTRAL[H+]=[OH–]

H+ H+

H+ OH– H+

H+ H+

OH– H+ H+

OH–

OH–

H+ H+OH–

OH– OH–

H+ H+H+

OH–

OH–

OH– OH–

OH–OH– H+

Incr

easi

ngly

BA

SIC

(Low

er c

once

ntra

tion

of H

+)

OH–

H+

14

13

Figure 2.15

– The pH of most cells • Is kept close to 7 (neutral) by buffers

– Buffers are substances that resist pH change

What are buffers?

• Buffers are substances that the body uses to prevent big shifts in pH.

• Either will release H+ ions or combine with H+ ions to keep the balance.

Bicarbonate is an example of one of the body’s important buffers

CONNECTION• Acid precipitation threatens the environment

– Some ecosystems are threatened by acid precipitation

– Acid precipitation is formed when air pollutants from burning fossil fuels

• Combine with water vapor in the air to form sulfuric and nitric acids

– These acids • Can kill trees and damage buildings

CHEMICAL REACTIONS•Chemical reactions change the composition of matter

– In a chemical reaction• Reactants interact, atoms rearrange, and products

result

2 H2O2 2 H2OFigure 2.17A

TYPES OF CHEMICAL REACTIONS

Chemical reactions happen every moment of everyday in every cell of every living organism.

• During chemical reactions either small molecules come together to form larger ones or large molecules break up.

• Whenever chemical reactions take place bonds form or bonds break and ENERGY is involved. The energy of the system changes .

FUNCTIONAL GROUPS

• These “functional groups” are attached (covalently bonded) to a carbon “backbone” or chains of carbons to form different biological molecules.

C-C-C-C-C-C-C-C-C-C- -OH hydroxyl group, forms sugars aldehyde group, forms sugars -COOH carboxyl group, found in sugars,

fats and amino acids -NH2 amino group, forms amino acids and

proteins

OXIDATION /REDUCTION REACTIONS (OIL RIG)• Oxygen is everywhere in our atmosphere and it

is very reactive.• Oxidation: Chemical reaction in which an atom loses

electrons while combining. Ex: burning anything (combustion) and oxidation (rusting)• The atom that loses the electrons is oxidized• Reduction: The gaining of electrons by another atom. The one accepting or receiving electrons is

reduced.

CONDENSATION REACTIONS and HYDROLYSIS REACTION

• Condensation or dehydration reactions: Water is taken out.

Cells put together large molecules this way. Enzymes remove an –OH (hydroxyl) from one molecule and a H from another, then a covalent bond is formed and water is formed. Ex: building proteins.

• Hydrolysis : Water is added. Breaking down the covalent bonds and splitting a

molecule into 2 or more parts. A H and –OH from a water molecule are attached to the exposed ends. Hydrolysis (breaking bonds) releases energy. Ex: digestion.

Endergonic and Exergonic reactions

• Exergonic: a chemical reaction that releases energy (energy out)

Ex: Cellular respiration, light display of a firefly,

Endergonic reaction: Chemical reaction that requires an input of energy. (energy in).

Ex: photosynthesis, building new molecules.

EXOTHERMIC and ENDOTHERMIC Reactions

• Reactions that give off heat energy are EXOTHERMIC

Ex: gas moving car, body using glucose

• Reactions that use or take in heat energy are ENDOTHERMIC

Ex; cooking

Questions

• 1. What caused the Brown Pelican to become an endangered species? Is it still one?

• 2. We divide the study of life into levels of biological organization. What are those levels starting with the smallest?

• 3. Organisms that provide food for an ecosystem are called______.

• 4. Those that recycle dead matter into simple chemicals are ______.

• 5. Chemical nutrient are _____ though an ecosystem, but energy_____.

• 6.What is the unit of structure and function of all life?