Biochemistry notes students

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.



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



 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.



 Electrons are negatively charged particles
that are located outside the nucleus.


• Atomic Number: number of protons in the
nucleus of an element (atom).

• 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



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



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



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.



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


6.3 Water and Solutions

Water’s 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.



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”: Water properties:
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



Heterogeneous Mixtures

 In a heterogeneous
mixture, the
components remain
distinct.

A salad is a heterogeneous mixture.



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 Food coloring dissolved in
water forms a homogenous

solvent. mixture.



Acids and Bases
 Excess of hydrogen ions (H+) are called acids.

 Excess of hydroxide ions (OH–) are called bases.


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



 Buffers are mixtures that can react with
acids or bases to keep the pH within a
particular range.


6.4 The Building Blocks of Life

Organic Chemistry
 The study of all
compounds containing
the element CARBON



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

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

Macromolecules
are also called
polymers!!!!

The 4 types of macromolecules:

NUCLEIC ACIDS
CARBOHYDRATES

LIPIDS PROTEINS



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

Section 2-3 Where found?
• 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

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 & (Liquid at room temp
“saturated” with Hydrogen & have double bonds.
atoms, single bonds) few Hydrogen atoms)

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

Saturated Fats Ex’s:

Unsaturated fats Ex’s:

•Some cooking oils
•Nuts
•Margarine
•Fish oils


6.2 Chemical Reactions

Reactants and Products
 A chemical reaction is the
process by which atoms or
groups of atoms in
substances are reorganized Chemical reaction
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. Physical reaction



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



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



 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)



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

 Ex: photosynthesis


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.



 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



 The active site specifically is shaped to
match the substrate and forms the enzyme-
substrate complex, which helps bonds in the
reactants to be broken and new bonds to
form.
 Factors such as pH, temperature, and enzyme
concentration

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