2.1 Atoms, Ions, and Molecules
KEY CONCEPT
All living things are based on atoms and their
interactions.
2.1 Atoms, Ions, and Molecules
Objectives
• Identify elements common to all living things
• Describe how ions form
• Compare ionic and covalent bonding
2.1 Atoms, Ions, and Molecules
Vocabulary
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Atom
Element
Compound
Ion
Ionic bond
Covalent bond
Molecule
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Proton
Neutron
Electron
Nucleus
Atomic Number
Atomic Mass
2.1 Atoms, Ions, and Molecules
Living things consist of atoms of different elements.
• An atom is the smallest basic unit of matter.
• An element is one type of atom.
Hydrogen atom (H)
H
Oxygen atom (O)
O
2.1 Atoms, Ions, and Molecules
• An atom has a nucleus and electrons.
– The nucleus has protons and neutrons.
– Electrons are in energy levels outside nucleus.
- The outermost energy level determines the activity of the atom
Oxygen atom (O)
Nucleus:
8 protons (+)
8 neutrons
outermost energy level:
6 electrons (-)
inner energy level:
2 electrons (-)
2.1 Atoms, Ions, and Molecules
Atoms want to be stable
• Energy levels want to be full of electrons
• Each level can hold a different number of electrons
– 1st energy level wants 2e– 2nd energy level wants 8 electrons
– 3rd energy level wants either 8 or 18
– Lower energy levels always fill up before higher
energy levels
If the energy level isn’t full, the atom is not stable
and will react with other atoms and form bonds!
2.1 Atoms, Ions, and Molecules
• A compound is made of atoms of different elements
bonded together.
– water (H2O)
_
O
H
+
H
+
2.1 Atoms, Ions, and Molecules
Atoms want to be stable
• Different atoms have different numbers of energy levels
• The outermost energy level of an atom is called its
valence shell
• Electrons in the outermost energy level are called
valence electrons
• It’s the valence electrons that determine
– what types of bonds will form
– How many bonds will form
2.1 Atoms, Ions, and Molecules
• A compound is made of atoms of different elements
bonded together.
– carbon dioxide (CO2)
2.1 Atoms, Ions, and Molecules
Different Compounds are held together by different
types of bonds
• Covalent Bonds
– Compounds held together by covalent bonds are
called molecules
• Ionic Bonds
• Hydrogen Bonds
• The type of bond that will form depends on the number of
valence electrons
Valence Electron Configuration
Hydrogen
1H
Mass number
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium Magnesium Aluminum
11Na
12Mg
13Al
Third
shell
2.1 Atoms, Ions, and Molecules
Atoms share pairs of electrons in covalent bonds.
• A covalent bond forms when atoms share a pair of
electrons.
– The number of covalent bonds depends on the
number of valence electrons an atom has to share
covalent bonds
Oxygen atom (O)
Carbon atom (C)
Carbon dioxide (CO2 )
Oxygen atom (O)
2.1 Atoms, Ions, and Molecules
• Covalent bonds are when atoms share electrons
• Sometimes its easier for an atom to gain or lose an
electron than to share
• Atoms that gain electrons
– Are called anions
– what kind of charge will an anion have?
• Atoms that lose electrons
– Are called cations
– what kind of charge will an cation have?
2.1 Atoms, Ions, and Molecules
Ions form when atoms gain or lose electrons.
• An ion is an atom that has gained or lost one or more
electrons.
• Ionic bonds form between oppositely charged ions.
Opposites Attract
gained electron
Na loses an
electron to CI
Sodium atom (Na)
Chlorine atom (CI)
ionic bond
Sodium ion (Na+)
Chloride ion (CI-)
2.1 Atoms, Ions, and Molecules
What distinguishes one element from another?
• The number of protons in the nucleus
2.1 Atoms, Ions, and Molecules
Describe the formation of an ionic compound
• One atom gives up an electron, another atom picks up
that electron
• The atom that loses the electron has a positive charge
• The atom that gains the electron has a negative charge
• The two oppositely charged ions are attracted to each
other and form an ionic bond
2.1 Atoms, Ions, and Molecules
What is the difference between an ionic and a covalent
bond?
• An ionic bond is formed due to the electrical attraction
between oppositely charged ions
• A covalent bond is formed by a shared pair of electrons
2.1 Atoms, Ions, and Molecules
How does a molecule differ from an atom?
• A molecule is made up of 2 or more atoms held together
by covalent bonds
2.1 Atoms, Ions, and Molecules
Explain why a Hydrogen atom can become either an ion
or a part of a molecule?
• A hydrogen atom has one unpaired electron in its outer
energy level
• The electron can either be lost to form an ion, or shared
to form a covalent bond
2.1 Atoms, Ions, and Molecules
A sodium atom has one outer electron, and a carbon
atom has 4 outer electrons. How might this difference
be related to types of compounds formed by atoms of
these 2 elements?
• An atom that has a nearly full or nearly empty energy
level (such as sodium) tends to form ions
• An atom in between (such as carbon) tends to share
electrons
2.2 Properties of Water
KEY CONCEPT
Water’s unique properties allow life to exist on
Earth.
2.2 Properties of Water
Objectives
• Recognize the importance of hydrogen bonding
• Explain why many compounds dissolve in water
• Compare acids and bases
2.2 Properties of Water
Vocabulary
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Hydrogen bond
Cohesion
Adhesion
Solution
Solvent
Solute
Acid
Base
pH
Hydrogen ion
2.2 Properties of Water
Life depends on hydrogen bonds in water.
• Water is the only common substance found naturally in
all three common states of matter and it is essential for all
life on Earth
• What kind of bonds are holding these 2 hydrogen atoms
to the oxygen in this compound?
2.2 Properties of Water
Life depends on hydrogen bonds in water.
• Its true that these are covalent bonds holding the
hydrogen atoms to the oxygen and so they are sharing
electrons
O
H
H
• BUT oxygen does not share the electrons equally with
the hydrogen atoms
• Electrons spend more time on the oxygen side than the
hydrogen side
• What kind of charge will oxygen have?
2.2 Properties of Water
Life depends on hydrogen bonds in water.
• Water is a polar molecule.
– Polar molecules have slightly charged regions.
_
O
H
+
H
+
– Nonpolar molecules do not have charged regions.
– Hydrogen bonds form between slightly
positive hydrogen atoms and slightly negative atoms.
2.2 Properties of Water
• Hydrogen bonds are responsible for three important
properties of water.
– high specific heat
– cohesion
– adhesion
2.2 Properties of Water
Specific Heat Capacity
• Specific Heat is the amount of heat per unit mass
required to raise the temperature by one degree Celsius
• Water has a high specific heat capacity
– This means it requires a lot of heat energy to raise the
temperature of water
– This allows water to moderate Earth's climate by
buffering large fluctuations in temperature
- Because water can absorb the heat from the air when its
hotter, and release the heat when its cooler outside
2.2 Properties of Water
Heat of vaporization
• The energy required to transform a given quantity of a
substance from a liquid into a gas
• Water has a high heat of vaporization
• Organisms exploit this in a process called evaporative
cooling
– As water evaporates it absorbs heat from the
environment, leaving it cooler
2.2 Properties of Water
Capillary Action and Surface Tension are products of
adhesion & cohesion
Cohesion
• Water molecules are
attracted to other water
molecules
• Water sticks to itself
Adhesion
• Water molecules are
attracted to other polar
molecules
• Water sticks to things
• EX: water sticks to the
side of you cold soda cup
on a hot day
2.2 Properties of Water
Capillary Action and Surface Tension are products of
adhesion & cohesion
Surface Tension
• A thin “skin” across the
surface of water due to
cohesion
•
https://www.youtube.com/watch?v=45yabrnryXk
Capillary Action
• water rises into a narrow
tube against the force of
gravity.
• Water adheres to the
inside wall of the tube
and surface tension tends
to straighten the surface
causing a surface rise
and more water is pulled
up through cohesion
2.2 Properties of Water
Many compounds dissolve in water.
• A solution is formed when one substance dissolves in
another.
– A solution is a homogeneous mixture.
– Solvents dissolve other substances.
– Solutes dissolve in a solvent.
solution
2.2 Properties of Water
• “Like dissolves like.”
– Polar solvents dissolve polar solutes.
– Hydrophilic: water loving
– Nonpolar solvents dissolve nonpolar solutes.
– Hydrophobic: water fearing
– Polar substances and nonpolar substances generally
remain separate.
– think oil (nonpolar) & water
– vinegar (polar) & water
2.2 Properties of Water
Some compounds form acids or bases.
• An acid releases a hydrogen ion (H+) when it dissolves in
water.
– high H+ concentration
– pH less than 7
stomach acid pH between 1 and 3
more acidic
2.2 Properties of Water
• A base removes hydrogen ions from a solution.
– low H+ concentration
– pH greater than 7
bile pH between 8 and 9
more basic
2.2 Properties of Water
• A neutral solution has a pH of 7.
pure water pH 7
2.2 Properties of Water
What causes a molecule to be polar?
• Unequal sharing of electrons between atoms
2.2 Properties of Water
How do polar molecules form hydrogen bonds?
• The oppositely charged regions of a polar molecule
attract other polar molecules, allowing positively charged
hydrogen atoms to bond to a negatively charged atom
2.2 Properties of Water
What are some of waters properties
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Its found in all three phases (solid, liquid, gas) on earth
High specific heat
High heat of vaporization
Adhesion
Cohesion
2.2 Properties of Water
How do organisms depend on waters properties to
survive
• Ice floats because its less dense allowing organisms to
live on the ice or under , and acts as an insulator
• Organisms utilize evaporative cooling (via sweating) to
maintain proper body temperature
• Plants use waters cohesive and adhesive properties to
perform capillary action and transpiration
• Animals and insects can walk or lay eggs on water due to
its surface tension
• Climate is regulated due to waters high specific heat
• Water is an important solvent in which many chemical
reactions take place
2.2 Properties of Water
What determines whether a compound will dissolve in
water
• Compounds that have charges, such as ionic
compounds (like table salt) and polar molecules (like
sugar) will dissolve in water
2.1 Atoms, Ions, and Molecules
Make a chart that compares acids and bases
Acids
• Donates protons
Bases
• Accept protons
• In solution has a high H+
ion concentration
• In solution has a low H+
concentration & a high
concentration of OH- ions
• pH below 7
• Has a pH above 7
2.1 Atoms, Ions, and Molecules
How do polar molecules differ from nonpolar
molecules? How does this difference affect their
interaction?
• Polar molecules have charged regions due to unequal
sharing of electrons.
• Nonpolar molecules do not have charged regions
because electrons are shared more equally
• The charge differences between polar and nonpolar
molecules tend to keep the molecules separate
2.1 Atoms, Ions, and Molecules
Describe an example of cohesion or adhesion that you
might observe in your daily life
• Cohesions: water beading on the surface of an object
• Adhesions: water sticking to the outside of a milkshake
cup on a hot day
2.1 Atoms, Ions, and Molecules
When sugars are broken down to produce usable
energy a large amount of heat is released. Explain how
the water inside a cell helps to keep the cells
temperature constant.
• Water has a high specific heat
– Specific heat: a measure of how much something
resists temperature changes
• Water in a cell can absorb a large amount of energy
before its temperature increases
2.3 Carbon-Based Molecules
KEY CONCEPT
Carbon-based molecules are the foundation of life.
2.3 Carbon-Based Molecules
Objectives
• Describe the bonding properties of carbon atoms
• Compare carbohydrates, proteins, lipids, and nucleic
acids
2.3 Carbon-Based Molecules
Vocabulary
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Monomer
Polymer
Carbohydrate
Monosaccharide
Lipid
Phospholipid
Starch
Cellulose
Protein
Amino acid
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Peptide bond
Nucleic acid
Nucleotide
Glycogen
Chitin
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
2.3 Carbon-Based Molecules
Carbon atoms have unique bonding properties.
• How many electrons does a carbon atom have?
• How many of those electrons are valence electrons?
• How many more electrons does carbon need to be
stable?
• How many covalent bonds do you think carbon will make
to accomplish this?
2.3 Carbon-Based Molecules
Carbon atoms have unique bonding properties.
• Carbon forms covalent bonds with up to four other atoms,
including other carbon atoms.
• Carbon-based molecules have three general types of
structures.
– straight chain
– branched chain
– ring
2.3 Carbon-Based Molecules
• Many carbon-based molecules are made of many small
subunits called monomers bonded together to form
polymers.
– Monomers are the individual subunits.
– Polymers are made of many monomers.
2.3 Carbon-Based Molecules
Four main types of carbon-based molecules are found in
living things.
• Carbohydrates are made of carbon, hydrogen, and
oxygen.
2.3 Carbon-Based Molecules
Four main types of carbon-based molecules are found in
living things.
• Carbohydrates include sugars and starches
– MonomersMonosaccharides
– Glucose
– Fructose
– Galactose
– Polymers Polysaccharides
– Starches
– Cellulose
– Glycogen
– Chitin
2.3 Carbon-Based Molecules
• Carbohydrates can be broken down to provide
energy for cells.
• Some carbohydrates are part of cell structure.
Polymer (starch)
Starch is a polymer of
glucose monomers that
often has a branched
structure.
Polymer (cellulose)
monomer
Cellulose is a polymer
of glucose monomers
that has a straight, rigid
structure
2.3 Carbon-Based Molecules
• Lipids are nonpolar molecules that include fats, oils, and
cholesterol.
– Many contain carbon chains called fatty acids.
– Fats and oils contain fatty acids bonded to glycerol.
Triglyceride
2.3 Carbon-Based Molecules
• Lipids have several different functions.
– broken down as a source of energy
– make up cell membranes
– used to make hormones
2.3 Carbon-Based Molecules
• Fats and oils have different types of fatty acids.
– saturated fatty acids
– unsaturated fatty acids
2.3 Carbon-Based Molecules
• Phospholipids make up all cell membranes.
– Polar phosphate “head”
– Nonpolar fatty acid “tails”
Phospholipid
2.3 Carbon-Based Molecules
• Proteins are polymers of amino acid monomers.
– Twenty different amino acids are used to build proteins
in organisms.
2.3 Carbon-Based Molecules
• Proteins are polymers of amino acid monomers.
– Twenty different amino acids are used to build proteins
in organisms.
– Amino acids differ in side groups, or R groups.
2.3 Carbon-Based Molecules
• Proteins are polymers of amino acid monomers.
– Twenty different amino acids are used to build proteins
in organisms.
– Amino acids differ in side groups, or R groups.
– Amino acids are linked by peptide bonds.
2.3 Carbon-Based Molecules
• Proteins differ in the number and order of amino acids.
– Amino acids interact to give a protein its shape.
Hemoglobin
hydrogen bond
– Incorrect amino acids change a protein’s structure
and function.
2.3 Carbon-Based Molecules
2.3 Carbon-Based Molecules
• Nucleic acids are polymers of monomers called
nucleotides.
2.3 Carbon-Based Molecules
• Nucleic acids are polymers of monomers called
nucleotides.
– Nucleotides are made of a sugar, phosphate
group, and a nitrogen base.
A phosphate group
deoxyribose (sugar)
nitrogen-containing molecule,
called a base
2.3 Carbon-Based Molecules
• Nucleic acids are polymers of monomers called
nucleotides.
– Nucleotides are made of a sugar, phosphate
group, and a nitrogen base.
DNA
– DNA stores genetic
information .
– RNA is used to build RNA
proteins.
2.3 Carbon-Based Molecules
What is the relationship between a polymer and a
monomer
• A polymer is a large molecule made up of many smaller
units called monomers that are linked together
2.3 Carbon-Based Molecules
Explain how both nucleic acids and proteins are are
polymers. Be sure to describe the monomers that make
up the polymers.
Proteins
Composed of
monomers called
amino acids
There are 20
different amino
acids to choose
from
Nucleic Acids
• They’re both
polymers
because
they’re both
made of
smaller units
bonded
together
Composed of
monomers called
Nucleotides
Each nucleotide
consists of a sugar,
phosphate group,
and nitrogenous
base
2.3 Carbon-Based Molecules
How are carbohydrates and lipids similar? How are they
different
Carbohydrates
Includes sugars
and starches
Shorter term
energy storage
Cellulose in plant
cell walls and
chitin in fungi cell
walls
Lipids
-Both
made of
C,H, & O
-Broken down as
a source of
energy
-Have some
structural
functions
Includes fats,
oils, and waxes
Longer term
energy storage
Phospholipids
in the plasma
membrane
2.3 Carbon-Based Molecules
Explain how the bonding properties of carbon atoms
result in the large variety of carbon-based molecules in
living things
• Carbon atoms are able to form 4 covalent bonds with
other atoms including other carbon atoms
• Many other types of atoms can bind to carbon, and many
different combinations are possible
2.3 Carbon-Based Molecules
Why might fatty acids, amino acids, and nucleic acids
increase the hydrogen ion (H+) concentration of a
solution? Explain your answer.
• These molecules are all acids
• Acids, by definition, increase the H+ ion concentration of
a solution, and there by lower the pH
2.4 Chemical Reactions
KEY CONCEPT
Life depends on chemical reactions.
2.4 Chemical Reactions
Objectives
• Describe how bonds break and reform during chemical
reactions
• Explain why chemical reactions release or absorb energy
2.4 Chemical Reactions
Vocabulary
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Chemical reaction
Reactant
Product
Bond energy
Equilibrium
Activation energy
Endothermic
Exothermic
2.4 Chemical Reactions
Bonds break and form during chemical reactions.
• Chemical reactions change substances into different ones
by breaking and forming chemical bonds.
– Reactants are changed during a chemical reaction.
– Products are made by a chemical reaction.
2.4 Chemical Reactions
• Bond energy is the amount of energy that breaks a bond.
– Energy is added to break bonds.
– Energy is released when bonds form.
• A reaction is at equilibrium when reactants and products
form at the same rate.
CO2 + H2O
H2CO3
2.4 Chemical Reactions
Chemical reactions release or absorb energy.
• Activation energy is the amount of energy that needs
to be absorbed to start a chemical reaction.
2.4 Chemical Reactions
• Exothermic reactions release more energy than they
absorb.
– Reactants have higher bond energies than products.
– Excess energy is released by the reaction.
2.4 Chemical Reactions
• Endothermic reactions absorb more energy than they
release.
– Reactants have lower bond energies than products.
– Energy is absorbed by the reaction to make up the
difference.
2.4 Chemical Reactions
Hydrogen peroxide (H2O2) breaks down into water (H2O)
and oxygen (O2).
A) Explain why this is a chemical reaction.
B) what are the reactants?
C) what are the products?
• A) it is a chemical reaction because different substances
are formed
• B) reactant = Hydrogen peroxide (H2O2)
• C) products = water (H2O) and oxygen (O2)
2.4 Chemical Reactions
How do endothermic and exothermic reactions differ?
• Endothermic reactions absorb energy because the
products have a higher bond energy than the reactants
have
• Exothermic reactions release energy because the
products have a lower bond energy than the reactants
have
2.4 Chemical Reactions
The process below is exothermic. What must be true
about the bond energies of the reactants and the
products? Explain.
6O2 + C6H12O6  6CO2 + 6H2O
• The bond energies of the reactants must be higher than
those of the products because energy is released.
2.4 Chemical Reactions
Why might it not always be possible to determine the
reactants and the products in a reaction? Explain your
answer in terms of chemical equilibrium.
• Depending on the concentrations of the reactants and the
products, both reactants and products may be formed at
the same time if the reaction is reversible.
• At equilibrium, reactants and products are formed at the
same rate
2.4 Chemical Reactions
A chemical reaction can start when enough activation
energy is added to the reactants. Do you think the
activation energy for chemical reactions in living things
is high or low? Explain your answer.
• The activation energy for reactions must be relatively low
because temperature can not be greatly increased in
living things.
2.5 Enzymes
KEY CONCEPT
Enzymes are catalysts for chemical reactions in
living things.
2.5 Enzymes
Objectives
• Explain the effect of a catalyst on activation energy
• Describe how enzymes regulate chemical reactions
2.5 Enzymes
Vocabulary
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Catalyst
Enzyme
Substrate
Active site
2.5 Enzymes
A catalyst lowers activation energy.
• Catalysts are substances that speed up chemical
reactions.
– decrease activation energy
– increase reaction rate
2.5 Enzymes
Enzymes allow chemical reactions to occur under tightly
controlled conditions.
• Enzymes are catalysts in living things.
– Enzymes are needed for almost all processes.
– Most enzymes are proteins.
2.5 Enzymes
• Disruptions in homeostasis can prevent enzymes from
functioning.
– Enzymes function best in a small range of conditions.
– Changes in temperature and pH can break hydrogen
bonds.
– An enzyme’s function depends on its structure.
2.5 Enzymes
• An enzyme’s structure allows only certain reactants to
bind to the enzyme.
– substrates
– active site
substrates
(reactants)
enzyme
Substrates bind to an
enzyme at certain places
called active sites.
2.5 Enzymes
• The lock-and-key model helps illustrate how enzymes
function.
– substrates brought together
– bonds in substrates weakened
Substrates bind to an
enzyme at certain
places called active
sites.
The enzyme brings
substrates together
and weakens their
bonds.
The catalyzed reaction forms
a product that is released
from the enzyme.
2.5 Enzymes
How does a catalyst affect the activation energy and rate
of a reaction
• A catalyst reduces the activation energy required to start
a reaction
• A catalyst speeds up the rate of chemical reactions
2.5 Enzymes
Describe how the interaction between an enzyme and its
substrates changes a chemical reaction
• An enzyme brings substrates close together and slightly
alters (weakens) the bonds within the substrates by
changing the shapes of the molecules so that they can
react
2.5 Enzymes
Some organisms live in very hot or acidic environments.
Would their enzymes function in a persons cells? Why
or why not?
• NO
• Those enzymes function optimally under different
conditions than those found in a person
2.5 Enzymes
Suppose that the amino acids that make up an enzymes
active site are changed. How might this change affect
the enzyme?
• The substrates would likely not bond to the enzyme
because the shape of the active site would change.
2.5 Enzymes
Organisms need to maintain homeostasis, or stable
internal conditions. Why is homeostasis important for
the function of enzymes?
• If homeostatic conditions, such as temperature, ionic
(salt) concentrations, or pH are not maintained, then the
hydrogen bonds that keep an enzyme in its correct shape
will weaken or break and the enzymes structure will
change.
Because enzymes function is determined by their structure,
changing their shape will affect their function