Protein Structure
• Molecular structure Textbook reference: Chapter 4 – pp. 71-79 (selected
• Peptide bonds sections as outlined below).
• Levels of protein structure Please work through these interactive online lecture notes
before attending Lecture 4.
• Protein folding
Of all the macromolecules, proteins are the most versatile. Almost every process that occurs in a
cell requires proteins. So, apart from having complex structures, proteins also have a variety of
functions.
• Structural proteins - can aggregate to help define a cell’s shape and fix organelles in
position.
• Pores and channels – are proteins inserted in cell membranes that allow ions and small
molecules to pass through.
• Enzymes – are proteins that catalyze metabolic reactions in cells
• Signaling proteins – help cells communicate with each other to coordinate function
Molecular Structure
Background textbook reading:
• Section 4.1 Molecular Structure of Proteins (pp. 71-73)
Proteins are typically very large molecules. They are polymers of amino acids linked together by
peptide bonds. What type of bonds are peptide bonds? COVALENT
An amino acid has a general structure shown below. Label the following on the diagram: R-
group, amino group, alpha (α) carbon, a carboxyl group
The three-dimensional structure of an amino acid looks
like this.
What is the difference between
illustrations ‘a’ and ‘b’ on the right?
Explain.
In Illustration 'b/ the original structure of the amino acid differs slightly, as the amino group (-NH3), gains a proton to
become (- NH3+), and the carbonyl group (- COO) loses a proton to become (-COO-) while illustration ‘a' is the original
structure of amino acid with no changes in its structure.
It is the R-group that makes each amino acid unique. R-groups are chemically diverse and give
amino acids their properties, so amino acids are typically classified according to the properties of
1
, their R-groups. These properties strongly influence protein structure such as how proteins fold
(i.e. their three-dimensional structure).
There are 20 amino acids that are the building blocks of all proteins.
Using Figure 4.2 on p. 73 of your textbook, complete the graphic below to summarize which
amino acids belong to which category. MEMORIZE
Hydrophilic Amino Acids Hydrophobic
Amino Acids
Basic Acidic Polar glycine (Gly), Special Amino Acids
alanine (Ala),
Lysine Aspartic Asparagine Glycine (Gly, G)
valine (Val),
(Lys, K) Acid (Asn, N)
leucine (Leu),
Proline (Pro, P)
(Asp, D) Glutamine isoleucine (Ile), Cysteine (Cys, C)
(Gln, Q)
Arginine proline (Pro),
(Arg, R) Glutamine Serine (Ser, S) phenylalanine
Acid (Phe), methionine
Threonine
Histidine (Glu, E) (Thr, T) (Met), and
tryptophan (Trp).
(His, H)
NOTE: you are not expected to know the chemical structures of the amino acids but you should
know which ones are in each category and why.
Peptide Bonds
Background textbook reading:
• Section 4.1 Molecular Structure of Proteins (pp.
73-74)
The formation of the peptide bond involves the release of
a water molecule. The carboxyl group of one amino acid
reacts with the amino group of the adjacent amino acid.
The C=O group in the peptide bond is the carbonyl group
and the N-H group is the amide group. Label these in the
diagram on the right.
Notice that the R-groups of each amino acid in the
peptide point in a different direction.
In the of polypeptide, the ends are chemically distinct.
One end is the amino end and the other is the carboxyl
end.
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• Molecular structure Textbook reference: Chapter 4 – pp. 71-79 (selected
• Peptide bonds sections as outlined below).
• Levels of protein structure Please work through these interactive online lecture notes
before attending Lecture 4.
• Protein folding
Of all the macromolecules, proteins are the most versatile. Almost every process that occurs in a
cell requires proteins. So, apart from having complex structures, proteins also have a variety of
functions.
• Structural proteins - can aggregate to help define a cell’s shape and fix organelles in
position.
• Pores and channels – are proteins inserted in cell membranes that allow ions and small
molecules to pass through.
• Enzymes – are proteins that catalyze metabolic reactions in cells
• Signaling proteins – help cells communicate with each other to coordinate function
Molecular Structure
Background textbook reading:
• Section 4.1 Molecular Structure of Proteins (pp. 71-73)
Proteins are typically very large molecules. They are polymers of amino acids linked together by
peptide bonds. What type of bonds are peptide bonds? COVALENT
An amino acid has a general structure shown below. Label the following on the diagram: R-
group, amino group, alpha (α) carbon, a carboxyl group
The three-dimensional structure of an amino acid looks
like this.
What is the difference between
illustrations ‘a’ and ‘b’ on the right?
Explain.
In Illustration 'b/ the original structure of the amino acid differs slightly, as the amino group (-NH3), gains a proton to
become (- NH3+), and the carbonyl group (- COO) loses a proton to become (-COO-) while illustration ‘a' is the original
structure of amino acid with no changes in its structure.
It is the R-group that makes each amino acid unique. R-groups are chemically diverse and give
amino acids their properties, so amino acids are typically classified according to the properties of
1
, their R-groups. These properties strongly influence protein structure such as how proteins fold
(i.e. their three-dimensional structure).
There are 20 amino acids that are the building blocks of all proteins.
Using Figure 4.2 on p. 73 of your textbook, complete the graphic below to summarize which
amino acids belong to which category. MEMORIZE
Hydrophilic Amino Acids Hydrophobic
Amino Acids
Basic Acidic Polar glycine (Gly), Special Amino Acids
alanine (Ala),
Lysine Aspartic Asparagine Glycine (Gly, G)
valine (Val),
(Lys, K) Acid (Asn, N)
leucine (Leu),
Proline (Pro, P)
(Asp, D) Glutamine isoleucine (Ile), Cysteine (Cys, C)
(Gln, Q)
Arginine proline (Pro),
(Arg, R) Glutamine Serine (Ser, S) phenylalanine
Acid (Phe), methionine
Threonine
Histidine (Glu, E) (Thr, T) (Met), and
tryptophan (Trp).
(His, H)
NOTE: you are not expected to know the chemical structures of the amino acids but you should
know which ones are in each category and why.
Peptide Bonds
Background textbook reading:
• Section 4.1 Molecular Structure of Proteins (pp.
73-74)
The formation of the peptide bond involves the release of
a water molecule. The carboxyl group of one amino acid
reacts with the amino group of the adjacent amino acid.
The C=O group in the peptide bond is the carbonyl group
and the N-H group is the amide group. Label these in the
diagram on the right.
Notice that the R-groups of each amino acid in the
peptide point in a different direction.
In the of polypeptide, the ends are chemically distinct.
One end is the amino end and the other is the carboxyl
end.
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