Unit 3: Biochemistry
Honors Biology
Monkemeier
Write down these questions:
Answer them on lined paper after viewing the
ppt and videos
 Draw and label the basic structure of an amino acid. Explain how the
20 different amino acids are different from each other.
 Explain and describe the four levels of organization within proteins.
Mention appropriate bonding and interactions and provide specific
examples. Explain the role of chaperonins.
 List and describe the different roles that proteins play within
organisms.
 Explain how enzymes relate to chemical reactions. Use the terms:
substrate, active site, allosteric site. How do the terms denaturation
and dissociation relate to enzymes. Explain the effect of each of the
following have upon enzymes: temperature, pH and concentration of
substrate or enzyme?
Proteins
Proteins are the most diverse
group of biological
macromolecules, both
chemically and functionally.
Functions of Proteins
 Functions of proteins include:
 Enzyme catalysis
 Defense
 Transport
 Support
 Motion
 Regulation
 Storage
Structure of Proteins
 Amino acids are the
subunits of proteins
 There are 20 different
amino acids.
 All amino acids have the
same basic structure.
 What is different among
the amino acids is the
“R” Group.
Amino Acid Structure
 The unique character of
each amino acid is
determined by its “R”
Group.
 The “R” Group also
determines the
chemistry of amino
acids.
Each amino acid affects the shape of a protein
differently, depending upon the nature of the “R” Group
Building Proteins
 Amino Acids are bonded together to build proteins
using dehydration synthesis.
 The covalent bond that results from dehydration
synthesis is known as a PEPTIDE BOND.
 When bonding together amino acids to build
proteins, the carboxyl group from one amino acid has
to match up with the amino group of the next amino
acid. This is so that dehydration synthesis can take
place.
Dehydration Synthesis and Peptide
Bonds
Polypeptide
 A protein is composed of one or more long
unbranched chains.
 Each chain is called a polypeptide and is composed of
amino acids linked together with peptide bonds.
Proteins Have Levels of Structure
The shape of a protein determines
the protein’s function.
The structure of proteins has
traditionally been discussed in
terms of a hierarchy with four
levels of structure: primary,
secondary, tertiary and
quaternary.
Primary Structure- Amino Acid
Sequence
 The primary structure of a protein is its
amino acid sequence.
 If one amino acid is substituted,
deleted or added to a protein, the entire
protein is affected.
 Any alteration in the normal sequence
of amino acids can have drastic effects
on the function of the protein.
Secondary Structure: Hydrogen
bonding patterns.
Hydrogen bonds can form between
the different amino acids within
the polypeptide chains.
Alpha helix
Beta Pleated Sheets
Secondary Structure: Alpha helix
Secondary Structure: Beta pleated
sheet
Tertiary Structure: Folds and Links
 The final folded shape of a globular protein
is called a protein’s tertiary structure.
 Ionic bonds between oppositely charged R
groups, disulfide bridges between R groups
containing sulfur, and weak forces of
attraction called van der Waals forces all
contribute to the folding of proteins.
Tertiary Structure: Folds and Links
Quarternary Structure: subunit
arrangements
 When two or more polypeptide chains
associate to form a functional protein, the
individual chains are referred to as subunits
of the protein.
 The arrangements of these subunits is
termed the quarternary structure.
Quarternary Structure
Motifs
 Motifs are similar substructures within
proteins.
 Even though two proteins may be
different, they may contain similar
motifs, or substructures that are the
same.
Domains
 Domains are functional units within the
larger structure or tertiary structure.
 Metaphor
 Amino acids are the letters in protein
language
 Motifs are words or phrases
 Domains are paragraphs
Chaperone Proteins
 Chaperone proteins help other proteins fold correctly.
 Many cells produce chaperone proteins after a cell has
been exposed to high temperatures, elevated
temperatures, high pH, etc.
 The disease Cystic Fibrosis is a hereditary disorder
which affects the chaperone proteins that help a vital
protein that moves ions across cell membranes fold
correctly.
 Protein clumping in the brain that causes Alzheimer
disease may also be due to faulty chaperone proteins.
Denaturation
 Proteins function in optimum temperature and pH
ranges.
 When proteins are exposed to temperatures and pH
ranges ABOVE their optimum range, the protein can
change shape.
 Changing the shape of the protein affects its ability to
function properly.
 Changing the shape of the protein denatures the
protein and sometimes renders it inactive.
Upcoming Discovering Factors
that affect Enzymes Lab
 After our long weekend - Discovering Factors which
affect enzyme activity. Determine if proteins are
affected by changes in pH, temperature, concentration
of enzyme, concentration or substrate.
 Enzymes can be denatured when exposed to
temperatures and pH’s outside their optimum range.
 Enzymes that are denatured have changed their shape.