Biochemistry Note-Taking Guide
**Read This First** - This Note-Taking Guide is meant to be used as you go through each of the Units in
Biochemistry. It is only effective when used with course materials, including all of the Essential Reading
material in Campbell Biology (), the course videos () and podcasts (), the Learning Check questions, and
the Unit Quizzes. We highly recommend that you print out this guide and use it to make your own notes
on the course by writing the vocabulary definitions and answering the questions in your own words. We
also recommend that you review your notes every day for all Units to keep the course material fresh in
your mind even as you learn new material in the course.
If there are definitions or questions you are unable to answer on your own, please click here to discover multiple options
for working with a Course Instructor. We would love to help you succeed in Biochemistry! {{click here if
you’d like a PDF version}}
***Unit 2: Amino Acids, Peptide Bonds, and Protein Structure***
Key Questions - You should be able to answer these upon completion of the
Page Section Vocabulary
Unit/Section. Please add your own notes as necessary.
Proteins are all constructed from the same set of 20 amino
acids, linked in unbranched polymers. The bond between
amino acids is called
Amino Acids,
a peptide bond, so a polymer of amino acids is called a
,12 Peptide Bonds, polypeptide. A protein is a biologically functional molecule
and Protein made up of one or more polypeptides, each folded and coiled
Structure
into a specific three-dimensional structure.
2.1 Amino Acids: The
13 Building Blocks of
Proteins
14 Subtopic: Chemical Electrons
Elements, Atoms, and Energy
Bonds—Optional Covalent
Review bonds
, Biochemistry Note-Taking Guide page 2
Ionic bonds
Hydrogen
bonds
- What is the basic structure of an amino acid? List the 4 groups and
describe what they look like.
An amino acid is an organic molecule with both an amino group and a
carboxyl group. At the center of the amino acid is an asymmetric carbon
atom called the alpha carbon. The R group, also called the side chain, differs
with each amino acid
- How do you identify the 3 different types of side chains:
Amino non-polar/hydrophobic, polar, and charged?
Carboxyl
15 Subtopic: Amino Hydrophobic
Acid Structure and Hydrophilic Hydrophobic has C atom and is not charged (found in protein
Chemical Properties Disulfide interior) Polar has S, N, or O atom and is not charged (found in
bonds protein exterior) Charged are positively or negatively charged
Zwitterions (found in protein exterior)
- What kind of bonds do each of the 3 different types of side
chains make? Hydrophobic have Hydrophobic bonds (weakest
kind of bonds)
Polar have Disulfide (S-strongest kind of bonds) or Hydrogen (N, O)
bonds Charged have Ionic bonds
, Biochemistry Note-Taking Guide page 3
To become functional proteins, polymers of amino acids (polypeptides) must
fold and take on a particular shape.
Primary – backbone of peptide chain formed by peptide bonds during
2.2 Levels of dehydration reaction
Protein Structure
17 Secondary – backbone atoms of peptide chain connected by hydrogen
bonds forming Alpha helix or Beta sheets
Tertiary – R group interactions via: hydrophobic interactions (weakest),
hydrogen bonds, ionic bonds or disulfide bonds (strongest)
Quaternary – R group interactions (like above), but with other polypeptide
chains
18 Subtopic: Polypeptides Polypeptide When two amino acids are positioned so that the carboxyl group of one is
and Functional Proteins s Peptide adjacent to the amino group of the other, they can become joined by a
bonds dehydration reaction, with the removal of a water molecule. The resulting
covalent bond is called a peptide
**Read This First** - This Note-Taking Guide is meant to be used as you go through each of the Units in
Biochemistry. It is only effective when used with course materials, including all of the Essential Reading
material in Campbell Biology (), the course videos () and podcasts (), the Learning Check questions, and
the Unit Quizzes. We highly recommend that you print out this guide and use it to make your own notes
on the course by writing the vocabulary definitions and answering the questions in your own words. We
also recommend that you review your notes every day for all Units to keep the course material fresh in
your mind even as you learn new material in the course.
If there are definitions or questions you are unable to answer on your own, please click here to discover multiple options
for working with a Course Instructor. We would love to help you succeed in Biochemistry! {{click here if
you’d like a PDF version}}
***Unit 2: Amino Acids, Peptide Bonds, and Protein Structure***
Key Questions - You should be able to answer these upon completion of the
Page Section Vocabulary
Unit/Section. Please add your own notes as necessary.
Proteins are all constructed from the same set of 20 amino
acids, linked in unbranched polymers. The bond between
amino acids is called
Amino Acids,
a peptide bond, so a polymer of amino acids is called a
,12 Peptide Bonds, polypeptide. A protein is a biologically functional molecule
and Protein made up of one or more polypeptides, each folded and coiled
Structure
into a specific three-dimensional structure.
2.1 Amino Acids: The
13 Building Blocks of
Proteins
14 Subtopic: Chemical Electrons
Elements, Atoms, and Energy
Bonds—Optional Covalent
Review bonds
, Biochemistry Note-Taking Guide page 2
Ionic bonds
Hydrogen
bonds
- What is the basic structure of an amino acid? List the 4 groups and
describe what they look like.
An amino acid is an organic molecule with both an amino group and a
carboxyl group. At the center of the amino acid is an asymmetric carbon
atom called the alpha carbon. The R group, also called the side chain, differs
with each amino acid
- How do you identify the 3 different types of side chains:
Amino non-polar/hydrophobic, polar, and charged?
Carboxyl
15 Subtopic: Amino Hydrophobic
Acid Structure and Hydrophilic Hydrophobic has C atom and is not charged (found in protein
Chemical Properties Disulfide interior) Polar has S, N, or O atom and is not charged (found in
bonds protein exterior) Charged are positively or negatively charged
Zwitterions (found in protein exterior)
- What kind of bonds do each of the 3 different types of side
chains make? Hydrophobic have Hydrophobic bonds (weakest
kind of bonds)
Polar have Disulfide (S-strongest kind of bonds) or Hydrogen (N, O)
bonds Charged have Ionic bonds
, Biochemistry Note-Taking Guide page 3
To become functional proteins, polymers of amino acids (polypeptides) must
fold and take on a particular shape.
Primary – backbone of peptide chain formed by peptide bonds during
2.2 Levels of dehydration reaction
Protein Structure
17 Secondary – backbone atoms of peptide chain connected by hydrogen
bonds forming Alpha helix or Beta sheets
Tertiary – R group interactions via: hydrophobic interactions (weakest),
hydrogen bonds, ionic bonds or disulfide bonds (strongest)
Quaternary – R group interactions (like above), but with other polypeptide
chains
18 Subtopic: Polypeptides Polypeptide When two amino acids are positioned so that the carboxyl group of one is
and Functional Proteins s Peptide adjacent to the amino group of the other, they can become joined by a
bonds dehydration reaction, with the removal of a water molecule. The resulting
covalent bond is called a peptide
