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BIO 1110- Biochemistry
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Composition of Matter

The “stuff” of the universe

Anything that has mass and takes
up space

Made of elements
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Elements – Unique substances that
cannot be broken down into
simpler substances by chemical
methods.
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What 4 elements make up 96% of the body?
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Atoms – Building blocks of
elements
•
•
Every element’s atoms differ
from all other elements.
Differences in atoms give each
element different physical and
chemical properties.
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Atomic Structure
Atoms are made of subatomic
particles.
-
+
+
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In an uncharged atom, the number of
_______ and the number of _______
are _______.
2 electrons
2 protons
-
+
-
+
He
Charges balanced
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Molecules and Compounds
Molecule- A combination of 2 or more
atoms held together by chemical bonds.
The atoms can be the same (H2) or
different (H2O).
•
Compound- A type of molecule
formed by a combination of 2 or
more different kinds of atoms like
H2O.
•
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is a water molecule.
Water is a compound.
is a hydrogen gas molecule.
Hydrogen gas is not a compound.
All compounds are made of molecules,
but not all molecules are compounds.
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Chemical Bonds
Electron shells, or
energy levels, surround
the nucleus of an atom.
Bonds are formed
using the electrons in
the outermost energy
level.

Each energy level
can hold a specific
number of electrons.

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Filling Electron Shells


Valence shell – Outermost electron energy level
Octet rule – Except for the first shell which is
full with two electrons, atoms interact in a
manner to have 8 electrons in their valence
shell (energy level)
Will this atom interact with others? What about this one?
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Types of Bonds
Ions- Charged atoms resulting from the
gain or loss of electrons.
•
Ionic bonds form between atoms by the
transfer of one or more electrons
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Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Covalent Bonds

Covalent bonds are formed by the sharing of two
or more electrons.

Electron sharing produces molecules.
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Hydrogen Bonds

More like attractions than bonds

Formed when a hydrogen atom (which is
already covalently bonded to an atom) is
attracted to another atom

Causes surface tension in water
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Hydrogen Bonds in Water
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Figure 2.10a
Organic Chemistry

Molecules containing carbon

Exception- CO, CO2 & HCO3- because they
are smaller, less complex molecules

Carbon is special because it is electroneutralnever loses nor gains electrons but always
shares electrons

Building blocks of cells

They include carbohydrates, lipids, proteins and
nucleic acids
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Carbohydrates: Sugars and Starches
Contain carbon, hydrogen, and oxygen in a
1:2:1 ratio
•
•
Monosaccharides: Simple sugars (glucose)
•
Disaccharides: Double sugars- 2
monosaccharides bonded together
(sucrose)
•
Polysaccharides: Many sugars- Polymer
of monosaccharides (starch)
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Major functions of carbs
Used by cells to make ATP (cell energy)

Extra carbs are stored in muscles and the liver as
glycogen

Cell identity markers

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Lipids

Also contain C, H, and O but contains less O than
carbs

Functions include:

Organ padding

Energy storage

Provide structure to the cell membranes

Sex hormones
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Proteins

Large molecules composed of combinations of 20
different amino acids.

Functions include:

Hormones

Antibodies

Cell membrane structure

Muscle structure

Enzymes

Characteristics (hair color, skin color, eye color)
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Structural Levels of Proteins


Primary – Linear- Amino acid sequence
Secondary – Twisted or bent primary
structure
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Structural Levels of Proteins


Tertiary –
superimposed
folding of
secondary
structures
Quaternary – Two
or more protein
chains linked
together in a
specific manner
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Enzymes

Proteins that act as biological catalysts (speed up
reactions) by lowering the energy needed for a
chemical reaction (activation energy)

Usually end in –ase

Act on a substance called a substrate
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Mechanism of Enzyme Action

Substrate binds to the enzyme at its active site. The
enzyme and substrate fit together like a lock and
key.

The enzyme-substrate complex undergoes internal
rearrangements that form the product(s).

The enzyme releases the product(s).

Enzyme is unchanged so it can act over and over
again.
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Active site
Amino acids
+
Enzyme (E)
Substrates (S)
Enzyme-substrate
complex (E-S)
H2O
Free enzyme (E)
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
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Figure 2.21
Nucleic Acids
 Composed of carbon, oxygen, hydrogen,
nitrogen, and phosphorus

Examples:

DNA

RNA

ATP
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DNA

Genetic code: Tells the cells what proteins to
make and when to make them.

Found inside the nucleus.
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RNA

Complementary copy of the DNA code.

Made in the nucleus and exits to the cytoplasm.

Used as instructions for building proteins.
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Transcription and Translation
Transcription=
Making RNA from
DNA
Translation=
Making proteins
from RNA
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings