Download Macromolecules pt 3

Four Levels of Protein
Structure
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Biological activity of protein is determined by
these levels
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Primary structure is the sequence of amino
acids in a polypeptide (Usually read N-C)
Secondary structures are localized folds or
helices that form within a region of a
polypeptide
Tertiary structures are larger folding events that
are stabilized by interactions between R groups
Quaternary structure is the interaction of
multiple polypeptides within one active proteins
Primary Structure
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Sequence of amino acids within
a single polypeptide
Are often similar among proteins
of similar function
Usually written from amino
terminus to carboxy terminus
Can also provide some insight
into additional structures by the
position of particular groups of
amino acids
Secondary Structure
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Localized within regions
of polypeptide
Stabilized by hydrogen
bonding
a helix-stabilized by
frequent polar groups
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Right handed helices
b-pleated sheets are
formed by consecutive
polar groups on two
regions of polypeptide
Tertiary Structure
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Large folding events that are
stabilized by interactions
between amino acids
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Hydrophobic interactions
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Disulfide bridge
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Very stable bond formed
between two distant cysteine
residues
Ionic interactions

-Hydrogen bonds form
between polar groups
Nonpolar regions generally
internalize in structure
Strong bond between
oppositely charged side groups
Quaternary Structure
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Only seen in compound
proteins
Interactions are
maintained between
polypeptide chains by
bonds similar to tertiary
structure
Function is often unique
to quaternary structure
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Individual components
are unable to
accomplish task alone
Protein Structure Revisited
Fig. 5-23
Denaturation
Normal protein
Renaturation
Denatured protein
Protein Conformation
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The 3D structure in which the protein is
biologically active is called the active conformation
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Denatured protein has lost its active conformation
Shape of a protein is consistent under identical
conditions
Proteins will attempt to find the lowest energy form
under conditions
Conditions that affect conformation

Solvent (polar versus non-polar),pH, temperature and
chemical agents (2-mercaptoethanol)
Protein summary
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Very important biological macromolecules that
perform a wide array of functions
Polymers of amino acids
20 natural amino acids that have distinct R side
groups
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The side groups determines the shape and
function of a polypeptide
There are four levels of structural organization
of proteins
Nucleic Acids
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Deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA)
Polymer of nucleotides
Store cellular information
Molecules of inherited information
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Basis for genetics
Often large, very complex molecules
Serve as templates for proteins
Help control regulation of cellular functions
Nucleotides
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Comprises:
A pentose
sugar
 A nitrogen
containing
base
 An organic
phosphate
group
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Bases
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Two kinds of bases
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Pyrimidines are
single ring
structures
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Purines are double
ring structures
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cytosine, thymine
and uracil
adenine and
guanine
In DNA G-C and
A-T interactionss
Pentoses
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Deoxyribose in DNA and Ribose in RNA
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Only difference is the lack of an Oxygen at carbon 2 in
deoxyribose
Ring structures
Nucleic Acid Structure
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Phosphate group is attached
to carbon 5 of pentose
Oxygen of Phosphate forms
a phosphodiester bond with
the OH group on carbon 3
of the pentose
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Strands have a 5’ end and a
3’ end
Fig. 5-27ab
5' end
5'C
3'C
Nucleoside
Nitrogenous
base
5'C
Phosphate
group
5'C
3'C
(b) Nucleotide
3' end
(a) Polynucleotide, or nucleic acid
3'C
Sugar
(pentose)
DNA vs RNA
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Both are important for cell function
DNA is double stranded and longer-lived
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Both can serve as a template for the synthesis of
the other
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RNA is single stranded and has shorter life
DNA to RNA is very common (transcription)
RNA to DNA occurs only with retroviruses
(reverse transcription)
Both have 5’-3’ orientations
DNA Double Helix
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Structure elucidated by Watson and
Crick
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Two strands are anti-parallel
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From work of Wilkens and Franklin
5’end of each strand aligns with 3’
end of complementary strand
Bases pair by hydrogen bonding
A-T (2 bonds)and G-C (3 bonds)
 Since strands are complementary
they serve as a template for opposite
strand
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Strands make Double Helix structure
(twisted ladder)