02 basic chemistry 2015 ss
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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.
© 2016 Pearson Education, Inc.
The image below shows a living thing.
A. True
B. False
© 2016 Pearson Education, Inc.
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
© 2016 Pearson Education, Inc.
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 . . .
© 2016 Pearson Education, Inc.
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.
© 2015 Pearson Education, Inc.
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:
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.
© 2015 Pearson Education, Inc.
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
© 2016 Pearson Education, Inc.
The Properties of WaterWater’s structure enables special functions:
• Being a good solvent
• Facilitating chemical reactions
• Being cohesive
• Moderating temperature
© 2016 Pearson Education, Inc.
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
© 2016 Pearson Education, Inc.
The Properties of WaterA good solvent
Water’s polar structureDissolves saltsDissolves other polar molecules
Hydrophilic: water-loving• E.g., alcohol
© 2016 Pearson Education, Inc.
The Properties of WaterA good solvent
Water’s polar structureWill not dissolve nonpolar molecules like lipidsHydrophobic: water-fearing• E.g., cooking oil
© 2016 Pearson Education, Inc.
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
© 2016 Pearson Education, Inc.
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.
© 2016 Pearson Education, Inc.
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
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
© 2016 Pearson Education, Inc.
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
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