Proteins

1
Proteins

• Proteios, Greek word meaning
• first place.

2
Protein

• Proteins account for 50 of the dry mass of most
  cells.
• Proteins are instrumental in almost everything
  organisms do.
• Support.
• Storage
• Transport
• Cellular communications
• Movement
• Defense against foreign substances.

3
Hormonal
Transport
Defensive
Contractile and motor
4
(No Transcript)
5
Polypeptides
Diverse as proteins are, they all are polymers
constructed from the same set of 20 amino acids.
Polymers of amino acids are called polypeptides.
A protein consists of one or more polypeptides
folded and coiled into specific configurations.
6
Amino Acid Monomers

• Amino Acids are organic molecules possessing both
  carboxyl and amino groups.

Central or Alpha Carbon
Amino Group
Carboxyl Group
hydrogen (H), amino group (NH2), carboxyl
group (COOH), and some side chain symbolized by
R.
R H O
N C C H OH
H
Side Chain or R
7
Nonpolar
Polar
Electrically Charged
20 Amino Acids Monomers
8
Essential amino acids The essential amino acids
are arginine (required for the young, but not for
adults), histidine, isoleucine, leucine, lysine,
methionine, phenylalanine, threonine, tryptophan,
and valine. These amino acids are required in the
diet. Plants, of course, must be able to make all
their amino acids. Humans, on the other hand, do
not have all enzymes required for the
biosynthesis of all of the amino
acids. Humans can produce 10 of the 20
amino acids. The others must be supplied in the
food. Failure to obtain enough of even 1 of the
10 essential amino acids, those that we cannot
make, results in degradation of the body's
proteinsmuscle and so forthto obtain the one
amino acid that is needed. Unlike fat and starch,
the human body does not store excess amino acids
for later usethe amino acids must be in the food
every day. The 10 amino acids that we can produce
are alanine, asparagine, aspartic acid, cysteine,
glutamic acid, glutamine, glycine, proline,
serine and tyrosine. Tyrosine is produced from
phenylalanine, so if the diet is deficient in
phenylalanine, tyrosine will be required as well.

9

• To form protein, the amino acids are linked by
  dehydration synthesis to form peptide bonds. A
  peptide bond is a covalent bond.
• The chain of amino acids is also known as a
  polypeptide. Some proteins contain only one
  polypeptide chain while others, such as
  hemoglobin, contain several polypeptide chains
  all twisted together.
• The sequence of amino acids in each polypeptide
  or protein is unique to that protein, so each
  protein has its own, unique 3-D shape or native
  conformation.
• For example, sickle cell anemia is caused by a
  change in only one nucleotide in the DNA
  sequence that causes just one amino acid in one
  of the hemoglobin polypeptide molecules to be
  different. Because of this, the whole red blood
  cell ends up being deformed and unable to carry
• oxygen properly.
•                                                 
                                                    
       

10
Polypeptide
11

• As a polypeptide chain forms, it naturally twists
  and bends into its native conformation.

12
One of the things that helps determine the
native conformation of a protein is the side
chains of all the amino acids involved.
13
Remember some amino acid side chains are
hydrophobic while others are hydrophilic. In this
case, the likes attract all the hydrophobic
side chains try to get together in the center
of the molecule, away from the watery
environment, while the hydrophilic side chains
are attracted to the outside of the molecule,
near the watery environment. Additi
onally, some of the hydrophilic side chains have
groups of atoms attached that make them acidic,
while others have groups attached that make them
basic. Side chains with acidic ends are attracted
to side chains with basic ends, and can form
ionic bonds. Thus, the side chains interacting
with each other help to hold the protein in its
native conformation.
14
Determining the Amino Acid Sequence of a
Polypeptide.

• Frederick Sanger (Cambridge) worked on the
  hormone insulin in the late 1940s 50s.

• He used protein digesting enzymes and other
  catalysts that break polypeptides at specific
  places rather than completely hydrolyzing the
  chains of amino acids.
• Treatment with one of these agents cleaves a
  polypeptide into fragments, (each consisting of
  multiple amino acid subunits). Separated by
  technique called chromatography.
• Hydrolysis with a different agent breaks the
  polypeptide at different sites, yielding a second
  group of fragments.
• Used chemical methods to determine the sequence
  of amino acids in the small fragments.
• Then he searched for overlapping regions among
  the pieces obtained by hydrolyzing with the
  different agents.

15
Example Cys-Ser-Leu-Try-Gln-Leu
Try-Gln-Leu-Glu-Asn We deduce from the
overlapping regions that the intake polypeptide
contains in its primary structure the following
segment. Cys-ser-Leu-Tyr-Gln-ASn Just as
we could reconstruct the sentence from the
collection of fragments with overlapping sequence
letters, Sanger was able to reconstruct the
com- plete primary structure of insulin. Since
then, most of the steps involved in sequencing a
polypeptide have been automated.
16
Protein Confirmation and Function

• The term polypeptide is not quite synonymous with
  the term protein.
• (like comparing a piece of yarn to a
  sweater)
• A functional protein is not just a polypeptide
  chain, but one or more polypeptides precisely
  twisted, folded, and coiled into a molecule of
  unique shape.
• It is the amino acid sequence that determines
  what three-dimensional conformation the protein
  will take.
• A proteins specific conformation determines how
  it works.
• The function of the protein depends on its
  ability to recognize and bind to some other
  molecule.

17
Four Levels of Protein Structure

• Primary Structure
• This is the sequence of amino acids, which
  form a chain connected by peptide bonds. The
  amino acid sequence of a protein determines the
  higher levels of structure of the molecule.
• A single change in the primary structure
• (the amino acid sequence) can have
• a profound biological change in the
• overall structure and function. If there
• are some cysteines in the amino-acid
• sequence, they often react two by two
• to form disulphide bridges. Disulphide
• bridges are part of the primary structure.
• The primary structure of a protein is its
  amino acid sequence and the disulphide bridges,
  i.e. all covalent connections in a protein.

18
Four Levels of Protein Structure

• Secondary Structure

19
Four Levels of Protein Structure

• Tertiary Structure

Tertiary structure refers to the
three-dimensional structure of the entire
polypeptide chain. The function of a protein
(except as food) depends on its tertiary
structure.
20
Four Levels of Protein Structure

• Quaternary Structure
• Complexes of 2 or more polypeptide chains held
  together by non-covalent forces but in precise
  ratios and with a precise 3-D configuration.
• A considerable range of quaternary structure is
  found in proteins.
• The forces that stabilize a quaternary structure
  are much the same as those that stabilize the
  secondary tertiary structure i.e. the
  non-covalent interactions, and most important in
  this case is the tendency for hydrophobic groups
  to combine so as to exclude water.

21

• Denaturation is when a protein loses its native
  conformation.
• denatured enzymes lose their catalytic power
• denatured antibodies can no longer bind
  antigen
• For example, egg white (also called albumen)
  contains a protein called albumin which is
  water-soluble. However, if heated, albumin
  becomes denatured and loses its ability to be
  water-soluble.
• There are several possible things that can
  denature proteins.
• changing the temperature (adding heat) (why
  fevers are dangerous)
• changing the pH or salt concentration of the
  solution
• putting the protein into a hydrophobic solvent.
• In a hydrophobic solvent, the amino acids with
  hydrophobic side chains would all try to go to
  the outside of the molecule, and all those with
  hydrophilic side chains would cluster in the
  center of the molecule. If a protein remains
  water-soluble when denatured (unlike albumin), it
  can return to its native conformation if/when
  placed back into a normal environment.

22
Denaturation and Renaturation
23
Protein Folding Problem

• Biochemists know the amino acid sequence of more
  than 875,000 proteins and the three-dimensional
  shapes of more than 7,000.
• Even with this many primary structures the rules
  of folding have not been figured out.
• Most proteins probably go through several
  intermediate stages on their way to a stable
  conformation, but looking at completed forms does
  not give us clues to how it was accomplished.
• Researchers have developed a way for tracking
• a protein through its intermediate stages of
  folding.
• Chaperonins (Chaparone proteins) , protein
  molecules that assist the proper folding of other
  proteins.
• Dont actually specify the correct final
  structure, but work by keeping the new
  polypeptide segregated from bad influences in
  the cytoplasmic environment while it folds
  spontaneously.

24
Protein Folding Problem cont.

• A simple protein molecule is built of thousands
  of atoms.
• X-ray Crystallography is an important method used
  to determine a proteins three-dimensional
  structure.
• Nuclear Magnetic Resonance (NMR) spectroscopy.

25
(No Transcript)