02 Basic Chemistry 2015 ss

PowerPoint Lecture prepared by Dr. Judi Roux,

University of Minnesota Duluth

Chapter 2

Definition of “Life”

Importance of Water

& Basic Biochemistry

© 2016 Pearson Education, Inc.

Learning Outcomes

• Describe the properties associated with living organisms.

• List the components of water and some of the properties that make it important in living organisms.

• Describe how atomic structure affects chemical bonding.

• Compare and contrast hydrogen, covalent, and ionic bonds.


The image below shows a living thing.

A. True

B. False


2.1 A Definition of LifeCharacteristics

• Common set of biological molecules• Composed of cells• Growth• Movement• Reproduction• Response to external environmental stimuli• Metabolism• Maintain homeostasis


2.1 A Definition of LifeDo nonliving things have any of those characteristics?

What about… fire? clouds? rocks? Zombies ? - That is, the zombies you see on TV . . .


Chemicals make up all organisms, and the physical environment

Chemicals made from atoms = fundamental unit of matter

Chemistry = study of interactions between chemicals = Chemical reactions

Element = substance composed of only one type of atom

ELEMENTS, ATOMS, AND MOLECULES

Living organisms are composed of about 25 chemical elements

About 25 different atoms are essential to all life- Make up the common components found in cells

Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter

CHNOPSCarbonHydrogenNitrogenOxygenPhosphorusSulfur

These six atomsmake molecules

http://images.tutorvista.com/content/cellular-micromolecules/chemical-components-of-cell.jpeg

Trace elements are essential to life, but occur in minute amounts and –• Vary in type, depending on the different, unique

functions necessary for a particular species• For example - Chromium, Iron, Iodine, Zinc, Copper

-to list just a few . . .

Trace elements are common additives to food and water

• Dietary deficiencies in trace elements can cause various physiological conditions

For example: Iodine deficiency causes many metabolic problemsThis woman cannot make the hormone thyroxine, and her thyroid gland swellsShe can die if she does not eat enough iodine

Atom = fundamental unit of matter

- consists of protons, neutrons, and electrons

Matter = takes up space

Element = matter made from only one type of atom, so has the properties of that atom

Compound = different types of atoms associated by chemical bonds

Elements combine to form compounds

Atoms combine in fixed ratios to form compounds having different properties than the individual atoms

Sodium Chlorine Sodium Chloride

Subatomic Particles

An atom is made up of protons and neutrons

• Located in a central nucleus

The nucleus is surrounded by electrons

• Arranged in electron shells

++

– –

+

–

2

2

2

Protons

Neutrons

Electrons

Massnumber = 4

++

2e–

Electroncloud

Nucleus

Differences in ElementsAtoms are distinguished from each other by their specific number of protons & how they interact with other atoms.

+

–

6

6

6

Protons

Neutrons

Electrons

Massnumber = 12

+ +

6e–

Nucleus

Electroncloud The number of protons

determines the number of electrons

Electrons determine how an atom can associate – bond – to other atoms

FYI: IsotopesThe number of neutrons in an atom may vary

Variant forms of an element are called isotopes

Some isotopes are radioactive – spontaneously fall apart to make other atoms and subatomic particles

Radioactive isotopes can help or harm usRadioactive isotopes are useful as tracers for monitoring the fate of atoms in living organisms

Basic Research - Biologists often use radioactive tracers to follow molecules as they undergo chemical changes in an organismMedical Diagnosis - Radioactive tracers are often used for diagnosis in combination with sophisticated imaging instruments

Dangers

Radioactive isotopes have many beneficial uses, but -

Uncontrolled exposure to them can harm living organisms

• Radioactivity = nucleus of an atom falls apart, releasing both high-energy particles and/or gamma rays that destroy other atoms

• Radioactivity can destroy molecules, too

• Groups of radioactive atoms decay over long time periods

Chemical Bond = Atoms Sharing ElectronsAtoms form bonds to:

- Fill outer electron shells- Neutralize charges

Electron arrangement determines the chemical properties of an atom

Electrons in an atom are arranged in shells, which hold the different numbers of electrons in different types of atoms

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)

Hydrogen Helium

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

First shell

Secondshell

Thirdshell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

The distribution of electrons determines an atom’s chemical properties

The number of electrons in the outermost shell, called the valence shell, determines the chemical properties of the atom.

Atoms whose outer shells are not full tend to interact with other atoms in ways that enable them to fill their valence shells.

These interactions usually result in atoms staying close together, held by attractions called chemical bonds.


Two types of chemical bonds:

Ionic = unequal electron sharing so that atoms carry a charge (become ions)

Covalent = electrons shared relatively equally in new, molecular shells that cover both atoms

Chemical Bond = Atoms Sharing Electrons

Atoms form bonds to:

- Fill outer electron shells

- Neutralize charges

1. Ionic bonds = 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 ionCl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

An electrical attraction between ions with opposite charges

Results in an ionic bond

Transfer of electron

NaSodium atom

ClChlorine atom Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

Na Cl ClNa

+ ––

–

Ionic Bonding Forms Crystals

Each ion is not specifically associated with a single ion of opposite charge, but several ions

The total charges balance - There are equal numbers of oppositely charged ions, arranged appropriately in the crystal

Na+

Cl–

Sodium and chloride ions - bond to form sodium chloride, common table salt

Beta Quartz SiO2

Zircon ZrSiO4

Cesium Chloride CsCl

Retrieved 2/1/2010 from: http://cst-www.nrl.navy.mil/lattice/index.html

Ions can arrange in many different ways to form various crystals:

http://cst-www.nrl.navy.mil/lattice/struk.picts/sio2b.s.png

http://cst-www.nrl.navy.mil/lattice/struk.picts/ZrSiO4.s.png

http://cst-www.nrl.navy.mil/lattice/struk.picts/b2.s.png

2. 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

Molecule = specific number of atoms sharing electrons in covalent bonds

Covalent bonds join atoms into molecules through electron sharing

In a covalent bond, two atoms, each with an unpaired electron in its outer shell, actually share a pair of electrons.

• Two or more atoms held together by covalent bonds form a molecule.

• E.g., a covalent bond connects two hydrogen atoms in a molecule of the gas H2.


Unequal electron sharing creates

polar moleculesA molecule is nonpolar when its covalently bonded atoms share electrons equally

A molecule is polar when one atom captures more electrons, most of the time• Atoms gain a partial ionic charge, but• NO atom gains a complete +1 or -1 charge -

In a polar covalent bond (e.g., water)Electrons are shared unequally between atoms, creating a polar molecule

(–) (–)

(+) (+)

O

HH

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

Weak ionic bonds between molecules that include a hydrogen atom are called hydrogen bonds

One water molecule will form weak ionic bonds - hydrogen bonds – with four other water molecules

Hydrogen bond(+)

(+)

H

H(+)

(+)

(–)

(–)

(–)(–)

O

A review of grade-school science:PROPERTIES OF MATTERMatter exists in one of three states -

SOLID = Particles (atoms, ions, molecules) associate and are fixed in position. Particles do not move relative to each other.

A solid maintains its own shape.

LIQUID = Particles stay associated, but can break that association to move relative to one another. - A liquid (fluid”) will take the shape of its container and stay on the bottom

due to gravity.

GAS = Particles move independently of each other – do not associate and will fill the container.

On earth, water exists in all three states – Living systems use all those types of water

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 bond

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–

IONIC AND COVALENT BONDS, The bottom line:

Crystals – ionic compounds - fall apart in water

- Ions carry charge & form ionic bonds

- Water forms weak ionic bonds with atoms having a charge

- Ionic bonds break in water

+

–

–

–

–

––

–

–

––+

++

++

Na+

+

Na+

Cl–

Ion insolution Salt

crystal

Cl–

Molecules behave as discrete units in water

- Atoms in molecules do not usually dissociate in water -Molecular bonds do not form ions – electrons shared equally

Small molecules dissolve in water when –They contain polar covalent bonds, &/or

They contain an ionic bond

Whereas -

caffeine glucose aspirinleucine

Large molecules form stable structures in water

Living systems are built of molecules, not crystals.

Lysozyme, a protein

DNA, a nucleic acid

tRNA bound to a protein

CHEMICAL REACTIONSChemical Reactions occur when atoms change their electron-sharing “partners”

In a chemical reaction

- Compounds or molecules (reactants) contact

- Electrons leave original bonds (bonds break)

- Electrons form new bonds between different atoms (products)

2 H2O2 2 H2O

Reactants

Products

Reactants must:

Have enough intrinsic energy to move with respect to each otherliquid or gas state or dissolved in a liquid

Physically contact – collide – with enough energy for electrons to leave their bonds

Contact in the correct orientation – the parts of the molecules that react must contact

Living cells carry out thousands of chemical reactions that rearrange matter in significant ways

Usually only one bond in the entire molecule reacts

CH3 CH3 CH3

H2C C CH C CH C CH CH CH CH CH C

C CH2

CH2

CH2

CH3CH3

C

CH2

H2C

CH CHCHCH CH

CH3CH3 CH3

CH CHC CC

C

CH3CH3

O2 4H

CH C CH C C

CH CH CH CH OH

H

H

CH3CH3

C

C

H2C C

CH2

H2C

CH3CH3 CH3

Vitamin A(2 molecules)

Beta-carotene

2

WATER’S LIFE-SUPPORTING PROPERTIES

The Properties of WaterHydrogen bonding

Weak ionic attraction between moleculesSlightly negative oxygen attracted to slightly positive hydrogen


The Properties of WaterWater’s structure enables special functions:

• Being a good solvent

• Facilitating chemical reactions

• Being cohesive

• Moderating temperature


The Properties of WaterSolution: a chemical mixture

• Solute: substance that dissolves in solvent• Solvent: substance that dissolves soluteWater can dissolve many solutes that carry a charge


The Properties of WaterA good solvent

Water’s polar structureDissolves saltsDissolves other polar molecules

Hydrophilic: water-loving• E.g., alcohol


The Properties of WaterA good solvent

Water’s polar structureWill not dissolve nonpolar molecules like lipidsHydrophobic: water-fearing• E.g., cooking oil


Living Systems are > 80% Water Molecules

Water is the solvent for ions and molecules

- Allows for movement of polar or charged chemicals for metabolism

Roles of Water in Living Systems- Result from the chemical properties of water molecules -

The Properties of Water

Facilitates chemical reactions

Water: allows contact between solutes for chemical reaction

• Chemical reactions: changes in chemical composition of substances

• Reactants: solutes that are changed• Products: result of the chemical reaction


WATER’S LIFE-SUPPORTING PROPERTIESHydrogen bonds make liquid water cohesive

• Due to hydrogen bonding

• Water molecules move from a roots to leaves = transpiration

Root hair

Flow

of w

ater

Soil particle

Water

Water uptake from soil

Adhesion

Cellwall

Cohesion,by hydrogenbonding

Xylemcells

Cohesion andadhesion in the xylem

Xylem sap

Mesophyll cells

Air space within leaf

Stoma

Outside air

Transpiration

Watermolecule

Insects can walk on water due to surface tension – H2O molecules between air and water

• Created by cohesive water molecules

The Properties of WaterModerating temperature

• Water absorbs heat energy.• Hydrogen bonds are

disrupted first.• Additional heat will raise

the water temperature.


Adhesion = attraction between particles

Water’s hydrogen bonds moderate temperatureWater’s ability to store heat moderates body

temperature and climate

It takes a lot of energy to disrupt hydrogen bonds -So water is able to absorb a great deal of heat energy without a large increase in temperature

As water cools, a slight drop in temperature releases a large amount of heat

A water molecule takes energy with it when it evaporates

• Leading to evaporative cooling

Ice is less dense than liquid water which causes ice to float• Floating ice protects

lakes and oceans from freezing solid, so organisms can survive winters

Image courtesy of: http://www.terragalleria.com/parks/np-image.romo0615.htmlRocky Mountain Nat’l Park

http://www.terragalleria.com/parks/np-image.romo0615.html

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)

The pH scale measures the

Relative amounts of hydrogen ions (H+) and hydroxide ions (OH–)

Acid: more H+ and less OH–

• pH lower than 7

Base: more OH– and less H+ • pH greater than 7

Neutral: equal H+ and OH–

• pH = 7; pure water


The pH of most cells is kept close to 7 (neutral) by buffersBuffers are substances that resist pH change

An acid or base generates ions that can attack and break chemical bonds in molecules!

Because acids & bases can break covalent bonds, cells use them to do that when needed!

Acid precipitation threatens the environmentSome ecosystems are threatened by acid precipitationAcid precipitation is formed when air pollutants from burning fossil fuels

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

• H2SO4 and HNO3 are formed

These acids can kill trees and damage buildings

02 Basic Chemistry 2015 ss

Education

Transcript of 02 Basic Chemistry 2015 ss