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Biochemistry Notes

Unit 1
Chapter 6

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Elements
An element is a pure substance that cannot
be broken down

Each element has a unique name and


symbol.

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds


The Periodic Table of Elements
Horizontal rows are called periods.
Vertical columns are called groups.

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Chemistry = study of matter.


Atoms are the building blocks of matter.
Neutrons and protons are located at the
nucleus of the atom.
Protons are positively charged particles.
Neutrons are particles that have no
charge.

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Electrons are negatively charged particles


that are located outside the nucleus.

6.1 Atoms, Elements, and Compounds

Atomic Number: number of protons in the


nucleus of an element (atom).

6.1 Atoms, Elements, and Compounds

Atomic Mass: the number of protons & neutrons


in the nucleus of an element (atom).
Find the neutrons only:
Atomic mass-atomic number=neutrons
Ex: Carbon Picture

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Isotopes
Atoms of the same element that have the
same number of protons and electrons but
have a different number of neutrons

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Compounds
A pure substance formed when two or more
different elements combine
Compounds cannot be broken down into
simpler compounds or elements by physical
means, must be a chemical reaction

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Chemical Bonds
Covalent bonds
Chemical bond that
forms when
electrons are
shared
A molecule is a
compound in which the atoms are held
together by covalent bonds.

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

Ionic Bonds
Electrical attraction between two oppositely
charged atoms or groups of atoms

Chapter 6

Chemistry in Biology

6.3 Water and Solutions

Waters Polarity
Molecules that have an unequal distribution
of charges are called polar molecules.
Polarity is the property of having two
opposite poles.
(Think of North & South Pole)
A hydrogen bond is a bond involving a
hydrogen atom and a fluorine, oxygen, or
nitrogen atom.

Chapter 6

Chemistry in Biology

6.3 Water and Solutions

Chapter 6

Chemistry in Biology

6.1 Atoms, Elements, and Compounds

van der Waals Forces


When molecules come close together, the
attractive forces between slightly positive
and negative regions pull on the molecules
and hold them together.
The strength of the attraction depends on
the size of the molecule, its shape, and its
ability to attract electrons.

Water properties:
Water is cohesive
Cohesion: sticks to itself
Ex: allows some insects & spiders
can walk on the surface
Water is adhesive
Adhesion: sticks to other things
Ex: capillary action-pulls column of
water up to the top of a plant

Water is called Universal


solvent: dissolves many other
substances due to polarity
Differences in charges pulls/pushes
substances apart (Like a magnet
attracts or repels other magnets)
Water exhibits evaporative
cooling: removes heat when it
evaporates from a surface
Ex: sweating cools skin
Water expands during freezing:
expands into crystal formation
releasing heat
Ex: ice floating on water

Water properties:

Chapter 6

Chemistry in Biology

6.3 Water and Solutions

Heterogeneous Mixtures
In a heterogeneous
mixture, the
components remain
distinct.

A salad is a heterogeneous mixture.

Chapter 6

Chemistry in Biology

6.3 Water and Solutions

Homogenous Mixtures
A mixture that has a uniform
composition throughout
A solvent is a substance in
which another substance is
dissolved.
A solute is the substance
that is dissolved in the
solvent.

Food coloring dissolved in


water forms a homogenous
mixture.

Chapter 6

Chemistry in Biology

6.3 Water and Solutions


Acids and Bases
Excess of hydrogen ions (H+) are called acids.
Excess of hydroxide ions (OH) are called bases.

Chapter 6

Chemistry in Biology

6.3 Water and Solutions


pH and Buffers
The measure of concentration of H+ in a solution
is called pH.

Acidic solutions have pH values 0-6.99.


Basic solutions have pH values 7.01-14
Neutral solutions have a pH value 7.00

Chapter 6

Chemistry in Biology

6.3 Water and Solutions

Buffers are mixtures that can react with


acids or bases to keep the pH within a
particular range.

Chapter 6

Chemistry in Biology

6.4 The Building Blocks of Life

Organic Chemistry
The study of all
compounds containing
the element CARBON

Chapter 6

Chemistry in Biology

6.4 The Building Blocks of Life


Carbon compounds can be in the shape of straight
chains, branched chains, & rings.

What is a macromolecule?
A giant molecule made up
of 100s or 1000s or smaller
units called MONOMERS

Macromolecules
are also called
polymers!!!!

The 4 types of macromolecules:

CARBOHYDRATES

LIPIDS

NUCLEIC ACIDS

PROTEINS

Chapter 6

Chemistry in Biology

6.4 The Building Blocks of Life

Carbohydrates
Made up of carbon, hydrogen, and oxygen

CARBOHYDRATES
Used as main source of energy
Building block: glucose (C6H12O6)
Sugars: quick source of energy
Monosaccharide-simple sugar, disaccharide-2,
polysaccharide-many
Two types:

Ex: glucose, lactose, fructose, sucrose


Starches: source of energy breaking down
slower
Ex: potatoes, pasta, bread, grains

Figure 2-13 A Starch

Where found?
Section 2-3

Cellulose: plant cell walls

Glycogen: animal liver

Go to
Section:

Nucleic Acids
Made up of H,O,N,C & P
Store and transmit genetic info in nucleus
Made up of nucleotides
Two types (examples): DNA & RNA

PROTEINS
Made up of N,C,H, O
Made up of groups called amino
acids (20 in nature)
proteins have a large variety of
sizes & shapes
If the shape changes, it
becomes a new protein
Examples: muscles, peanuts,
soybeans

Chapter 6

Chemistry in Biology

6.4 The Building Blocks of Life

LIPIDS
Made up mainly of C & H
Used to store energy,
insulation & protection
Usually not soluble in
water
Made up of long chains of
fatty acids

Contrasting Lipids
Lipids/Triglyceride

Fats
(Mostly solid at room temperature)

Saturated

Unsaturated

(Solid at room temp &


saturated with Hydrogen
atoms, single bonds)

(Liquid at room temp


& have double bonds.
few Hydrogen atoms)

Oils
(Liquid at room temperature &
Considered mostly unsaturated
fats)

Saturated Fats Exs:

Unsaturated fats Exs:


Some cooking
oils
Nuts
Margarine
Fish oils

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions


Reactants and Products
A chemical reaction is the
process by which atoms or
groups of atoms in
substances are reorganized
into different substances.
Clues that a chemical
reaction has taken place
include the production of
heat or light, and formation
of a gas, liquid, or solid.

Chemical reaction

Physical reaction

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

Chemical Equations
Chemical formulas describe the substances in
the reaction and arrows indicate the process of
change.
Reactants are the starting substances, on the
left side of the arrow.
Products are the substances formed, on the
right side of the arrow.

Dehydration Synthesis
http://www.youtube.com/watch?v=UyDnnD3fMaU

A chemical reaction that builds molecules


by losing water molecules (H2O)

Before

After

Hydrolysis
Chemical reaction splitting a compound
into 2 by adding water (H2O)
Before

After

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

Energy of Reactions
Activation energy:
the minimum
amount of energy
needed for reactants
to form products in a
chemical reaction.

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

This reaction is
exothermic and
released heat energy.
The energy of the
product is lower than
the energy of the
reactants.
Ex. Na+ + Cl- =NaCl
(salt)

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

This reaction is
endothermic and
absorbed heat energy.
The energy of the
products is higher
than the energy of
the reactants.
Ex: photosynthesis

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

Enzymes
A catalyst is a
substance that lowers
the activation energy
and speeds up a
reaction
It does not increase how
much product is made and it can be re-used
over and over again
.Enzymes are biological catalysts.

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions


The reactants that bind to the enzyme are called
substrates.
The specific location where a substrate binds on an
enzyme is called the active site.
Fits together like a lock and key

Chapter 6

Chemistry in Biology

6.2 Chemical Reactions

The active site specifically is shaped to


match the substrate and forms the enzymesubstrate complex, which helps bonds in the
reactants to be broken and new bonds to
form.
Factors such as pH, temperature, and
enzyme concentration