Download Proteins

Macromolecules 3:
Proteins
Your Assignment
Your Protein Structure Assignment
1. Define proteins and their function
2. What is an amino acid (monomers joined via
dehydration synthesis)
3. How is a peptide bond formed?
4. What are the main uses of proteins in cells
(plants and animals)??
Your Protein Shape Assignment
1. What are the various levels of protein ‘shape’?
(primary, secondary, tertiary, quaternary)
2. How does structure relate to function with
regard to proteins?
3. What does it mean to denature a protein?,
Give one or more example.
Additional Resources (1)
• The Tree of Life, proteins and DNA module
Additional Resources (2)
Protein structure and conformation links
• Molecular Workbench DNA and protein
module
• http://www.youtube.com/watch?v=iaHHgEoa
2c8&feature=related
• http://www.youtube.com/watch?v=Q7dxi4ob
2O4&feature=related
Protein Functions
Proteins
• > 50% of the dry mass of a cell is
protein
Proteins are used for:
• Structural support
• Energy storage
• Transport of other substances
• Signalling from one part of the
organism to another
• Movement
• Defence against foreign substance
• Enzymes
• Humans have tens of thousands of
different proteins
• Most structurally sophisticated
molecule, due to unique 3D shape
or conformation
Amino Acid (Monomers)
 Amino acid structure:
NH3 - C - COOH
 Amino acids differ
due to the R
(functional) group
 The structure of the
R-group determines
the chemical
properties of the
amino acid
Proteins
Chemical composition C-H-O-N-(S)
Proteins are made up of smaller monomers called AMINO ACIDS
Amino Acids differ ONLY in the type of R (functional) group they
carry
Amino acids composed of 3 parts
1. Amino Group
2. Carboxylic group
3. Functional ®-group (Makes 20 different amino acids)



20 Amino Acids
Hydrophilic Amino Acids
Polar uncharged amino acids are hydrophilic &
can form H-bonds
Serine
Threonine
Glutamine
Asparagine
Tyrosine
Cysteine
Hydrophobic Amino Acids
Nonpolar amino acids are hydrophobic and are usually
found in the center of the protein. They also found in
proteins which are associated with cell membranes.
 Glycine
 Alanine
 Valine
 Leucine
 Isoleucine
 Methionine
 Phenylalanine
 Tryptophan
 Proline)
Electrically charged Amino Acids
The electrically charged amino acids have
electrical properties that can change depending
on the pH.
Aspartic Acid
Glutamic Acid
Lysine
Arginine
Histidine
Special Amino Acids
 Cysteine can form covalent disulfide bonds
 Proline had a unique structure and causes kinks in
the protein chain
Amino Acids link together to form
polypeptides
• 2 Amino Acids form a
covalent bond, called a
PEPTIDE BOND,through
a condensation reaction
to form a dipeptide
• Multiple amino acids can
bond to each other one
at a time, forming a long
chain called a
POLYPEPTIDE
Peptide Bonds –
link amino acids
Protein shape
• Each protein has a specific,
and complex shape
• Proteins are composed of
one or more polypeptides
• Different shapes allow
proteins to perform
different functions
Protein Shape Determines Function
• Proteins with only primary and secondary structures are called
fibrous proteins (claws, beaks, keratin, wool, collagen,
ligaments, reptile scales)
• Proteins with only 1,2,3 shapes are called globular
proteins
• If a protein is incorrectly folded, it can’t function correctly
• Not understood how proteins fold themselves, seem to have
molecules called chaperone proteins or chaperonins that
assist others
• A protein is denatured when it loses its shape and therefore its
ability to function correctly
21
20
Four Levels of Protein Structure/
Conformation
1. Primary - unique linear
sequence in which amino acids
are joined, can have dire
circumstances if changed (insulin)
2. Secondary - refers to three
dimensional shapes that are the
result of H bonding at regular
intervals, due to interactions
between the amino acid
backbones
• alpha helix is a coiled shape
• beta pleated sheet is an
accordion shape
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3. Tertiary
Complex 3-D globular shape due to
interactions between R groups of
amino acids in it
• Globular proteins such as
enzymes are held in position
by these interactions
4. Quaternary
Consist of more than one
polypeptide chain subunits,
associated with interactions
between these chains
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Protein Conformation
Primary Structure – sequence of amino acids
Secondary structure – Folding and coiling due
to H bond formation between carboxyl and
amino groups of non-adjacent amino acid. R
groups are NOT involved.
Tertiary structure – disulfide bridges, ionic
bonding, or H-bonding of R-groups
Quaternary structure – 2+ amino acid chains
R- group interactions, H bonds, ionic
interactions
Primary Structure
• A unique sequence of amino
acids in a long polypeptide
chain
• Any changes in primary
structure can affect a protein’s
conformation and its ability to
function
• Example: Sickle cell anemia
Primary structure
• The sequence of amino acids
• Involves peptide bonds between the carboxyl and amine groups
LYS
VAL
PHE
GLY
ARG
CYS
Sickle cell anaemia
• Sickling occurs
due to a
mutation of the
Hb gene,
associated with
replacement of
glutamic acid by
valine
Secondary Structure
• Segments of the
polypeptide strand
repeatedly coil or fold in a
pattern which contributes
to the overall conformation
• Made by hydrogen bonds
between the backbone of
the amino acids (amino
group and carboxyl groups)
Structures formed include:
• α-helices: area with a
helical
or spiral shape. Held
together
by H bonds between
every 4th amino acid
• β-pleated sheets: area
where 2 or more
regions of the
polypeptide chain lie in
parallel
Secondary Structure
Secondary structure
• The amino acids in the primary structure can bond together
to form :
• a) An alpha helix
b) a beta pleat
• The bonds involved are hydrogen bonds
• Large proteins will have regions containing both structures
Tertiary Structure
Made of irregular contortions from interactions between
side chains (R groups)
1. Hydrogen Bonds: between polar side groups
2. Ionic Bonds: between positively and negatively charged
side chains
3. Hydrophobic Interactions: non-polar side chains end up
on the inside of a protein, away from water—caused by
water excluding these side chains from
H bond interactions. Once together, held in place by
dipole-dipole interactions
4. Disulfide Bridges: strong covalent bonds between
cytosine’s sulfhydryl (-SH) groups
TERTIaRY STRUCTURE
• The protein molecule undergoes further twisting
and folding to form a 3 dimensional shape
• The structure is held in place by interactions
between R-groups of the different amino acids
Tertiary
Structure
Quaternary Structure
The overall protein structure that results
from the aggregation of 2 or more
polypeptide subunits
QUATERNARY STRUCTURE
• Proteins can contain more than one protein chain
• E.g. immunoglobulins (form antibodies)
Chain 3
Chain 2
Chain 1
• The bonds involved are the same as those for tertiary
structure
Review: The Four Levels of Protein
Folding
Denaturing of Protein
Proteins can be denatured by:
• Transfer from aqueous solution to an organic
solvent (e.g. chloroform)
• Any chemical that disrupts H-bonds, ionic bonds,
& disulfide bridges
• Excessive heat
• Changes in pH
Denaturation
• Protein conformation depends on the physical and chemical
conditions of the protein’s environment
• pH, salt concentration, temperature, and other aspects of the
environment (aqueous or organic solvent) can unravel or change the
conformation of the protein.
• Change in protein shape causes it to lose its function
• Some proteins can renature and reform their conformation, other
cannot.
TESTING FOR PROTEINS
• Measure out 2cm3 of test solution into a test
tube
• Add 2 cm3 of Biuret solution
• Shake and record colour change for each
sample
• Positive result = colour change from blue to
lilac