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013 Lecture 3: Biochemistry II 2/8/16

Section 3.2 What are the chemical structures and functions of
proteins?
Proteins are polymers of amino acids. The sequence of amino acids in a
protein determines its primary structure. Secondary, tertiary, and
quaternary structures arise through interactions among the amino acids. A
protein’s three-dimensional shape and exposed chemical groups establish its
binding specificity for other substances.

The functions of proteins include support, protection, catalysis, transport,

defense, regulation, and movement.

• Proteins consist of one or more polypeptide chains, which are

polymers of amino acids. Four atoms or groups are attached to a
central carbon atom: a hydrogen atom, an amino group, a carboxyl
group, and a variable R group. The particular properties of each
amino acid depend on its side chain, or R group, which may be
charged, polar, or hydrophobic.
• Peptide linkages, also called peptide bonds, covalently link amino
acids into polypeptide chains. These bonds form by condensation
 reactions between the carboxyl and amino groups.

• The primary structure of a protein is the sequence of amino acids

in the chain. This chain is folded into a secondary structure,
which in different parts of the protein may form an alpha helix or a
 beta pleated sheet. Hydrogen bonding stabilizes the structure.

• Hydrophobic side chains aggregate in the interior of a protein,

folding the protein.
• Disulfide bridges and noncovalent interactions between amino
acids cause polypeptide chains to fold into three-dimensional
tertiary structures. Covalent disulfide bridges can form between
specific cysteine side chains (see Figure 3.5), holding a folded
polypeptide in place. The tertiary structure is the biologically active
form. They form the overall shape of a single protein. Weak,
noncovalent interactions allow multiple polypeptide chains to form
quaternary structures.
• X-ray crystallography: method of determining the arrangement
of atoms within a crystal.
 • Heat, alterations in pH, or certain chemicals can all result in a
protein becoming denatured. This involves the loss of tertiary
and/or secondary structure as well as biological function.
• The specific shape and structure of a protein allows it to bind
noncovalently to other molecules. In addition, amino acids may be
modified by the covalent bonding of chemical groups to their side
chains. Such binding may result in the protein changing its shape.
• Chaperone proteins enhance correct protein folding and prevent
inappropriate binding to other molecules.
o Misfolded proteins can be pathogenic

A single amino acid change in primary protein structure causes sickle-cell

anemia.

Section 4.1: What are the chemical structures and functions of

nucleic acids?
The nucleic acids DNA and RNA are polymers made up of nucleotide
monomers. The sequence of nucleotides in DNA carries the information that
is used by RNA to specify primary protein structure. The genetic information
in DNA is passed from generation to generation and can be used to
understand evolutionary relationships.

The unique functions of the nucleic acids—DNA and RNA—are information

storage and transfer. DNA is the hereditary material that passes genetic
information from one generation to the next, and RNA uses that information
to specify the structures of proteins.
• Nucleic acids are polymers of nucleotides. A nucleotide consists of
a phosphate group, a pentose sugar (ribose in RNA and
deoxyribose in DNA), and a nitrogen-containing base.
o Molecules consisting of a pentose sugar and a nitrogenous
base—but no phosphate group—are called nucleosides.
• In DNA, the nucleotide bases are adenine (A), guanine (G),
cytosine (C), and thymine (T). Uracil (U) replaces thymine in
RNA. C, T, and U have single-ring structures and are pyrimidines.
A and G have double-ring structures and are purines.
• The nucleotides in DNA and RNA are joined by phosphodiester
linkages involving the sugar of one nucleotide and the phosphate
of the next, forming a nucleic acid polymer.
o DNA polymerase is used to assemble nucleotides.
 • Complementary base pairing due to hydrogen bonds between A
and T, A and U, and G and C occurs in nucleic acids. In RNA, the
hydrogen bonds result in a folded molecule. In DNA, the hydrogen
bonds connect two strands into a double helix.
• The information content of DNA and RNA resides in their base
sequences.
• DNA is expressed as RNA in transcription. RNA can then specify
the amino acid sequence of a protein in translation.

More thermal energy is needed to break apart DNA since hydrogen bonding
is strong.
DNA is a polymer – can be infinitely long. Human chromosome I has 250
million base pairs.
Nucleotides can play roles as carriers in the synthesis and breakdown of
carbohydrates and lipids.
The overall process of transcription and translation is called gene
expression.
Sanger DNA Sequencing allowed us to understand genetic diversity in totally
new ways. It was primarily used to help with the sequencing of the human
genome.
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