Proteins

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• Proteins

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Proteins / Polypeptides
3-D SHAPE!!
3-D SHAPE!!
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• The functional molecules of life

3-D SHAPE!!
3-D SHAPE!!
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• What are proteins?
• Proteins are amino acid polymers folded into
  specific three dimensional shapes.
• A protein structure determines its function.

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• Are proteins of different types?
• Enzymes ?
  biological catalysts
• 
  Immunoglobulins ? protect against foreign
• 
  microbes cancer cells
• Haemoglobin ?
  oxygen carrier
• Proteins
• Keratin ?
  formation of hair nails
• Fibrin ?
  essential for blood clotting
• Collagen ?
  formation of bones, ligaments
• 
  tendons

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• What are the building units of proteins?
• These are called the amino acids.
• What is a residue?
• When two or more amino acids combine to form a
  peptide, the elements of water are removed, and
  what remains of each amino acid is called a
  residue.

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• The general structural formula of amino acids

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• What are the two functional groups that amino
  acids posses?
• Amino acids posses both, the acidic (carboxyl)
  and the basic (amino) functional groups.

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Amino acids When dissolved in water the carboxyl
group donates an H ion to the amino group, so
both groups are ionized.
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• Acidic and basic amino acids
• Acidic amino acids posses a carboxyl group on
  their side chain (R), while basic amino acids
  have an amino group on the side chain (R).
• Polar
  (hydrophilic)
• amino acids may be
• 
  Nonpolar (hydrophobic)
• Charged
  (acidic or basic)

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• How many are the amino acids?
• There are 20 important amino acids used in
  protein synthesis, 8 of which are essential
  amino acids, meaning that the body cant
  synthesize.

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• What is a proline kink?
• Proline is the only amino acid whose side chain
  (R) forms a covalent bond with its amino group,
  and this results in what's called the proline
  kink.

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• How do amino acids bond together and what is the
  name of the bond (linkage)?

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• What determines the final shape (conformation) of
  the protein polymer?
• The final conformation of the protein is
  determined by the sequence of the amino acids it
  contains.

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• What is an amino terminus (A-terminus)?
• An amino terminus is the free amino group at one
  end of the polypeptide.
• What is a carboxyl terminus (C-terminus)
• A carboxyl terminus is the free carboxyl
• group at one end of the polypeptide.

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• Globular Proteins
• Are composed of one or more polypeptide chains
  that take on a rounded or spherical shape.
• Many enzymes and other functional proteins are
  globular.
• collagen
• e.g.
• keratin
• haemoglobin

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• Globular proteins may be described in terms of
  four levels of structure
• 1) The primary structure of protein
• 2) The secondary structure of protein
• 3) The tertiary structure of protein
• 4) The quaternary structure of protein

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• What is the primary structure of protein?
• Is the of amino acids in the
  polypeptide chain.

sequence
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STRUCTURE

• Primary (1º)
• Description The linear sequence of amino acids
  (AAs) as determined by the genetic code (DNA).
• Bonding Covalent peptide bonds between AAs.

H2O
H2O
H2O
H2O
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• What is the secondary structure of protein?
• In certain regions, a hydrogen bond forms between
  the electronegative oxygen of the carboxyl group
  of one peptide bond and the electropositive
  hydrogen of an amino group, that is four bonds
  away.
• 1) ahelix A type of polypeptide secondary
  structure characterized by a tight coil that is
  stabilized by hydrogen bonds.

a helix
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• 2) ß-pleated sheet polypeptide secondary
  structure that form between parallel stretches of
  a polypeptide, and are (the stretches) stabilized
  by hydrogen bonds.

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STRUCTURE

• Secondary (2º)
• Description The twisting and folding of the
  linear primary (1º) structure.
• Bonding Hydrogen bonds between charged AAs.
• Forms

triple helix
(e.g. keratin)
(e.g. fibrin)
(e.g. collagen)
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• What is the tertiary structure of protein?
• Is the complex folding (super coiling) of the
  polypeptide that is stabilized by side chain
  interactions (R-group - R-group interactions)
  that include all of the following
• Ionic bonds between oppositely charged side
  chains
• Hydrogen bonds between certain polar side chains
• Van Der Waals forces between non-polar groups
• Proline kinks
• Disulfide bridges when the sulfur containing
  R-groups of two cysteine residues are close they
  form a disulfide bridge (-S-S-) these are strong
  stabilizers of the tertiary structure

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• Disulfide bridges

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• What is the quaternary structure of protein?
• Is the clustering (aggregation) of two or more
  polypeptides of the tertiary structure.

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?
?
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• What is protein denaturation?
• Protein denaturation is the change in the
  three-dimensional shape of a protein.
• Denaturation could be due to changes in
• Temperature (heat denatures the protein in hair
  allowing to straighten curly hair, barbecuing
  meat boiling an egg)
• pH (gastrin works best at pH 2 and is denatured
  in the small intestine at pH 10)
• Ionic concentration
• Exposing the protein to liquids (water, alcohol)

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• What are chaperone proteins?
• Chaperone proteins are special proteins that aid
  a growing polypeptide to fold into the tertiary
  structure.

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• Nucleic Acids
• The two nucleic acids DNA and RNA are
• essential for all living things.
• DNA consists of sugar, phosphate groups
• linked together through sugar phosphate
• Bonds, and four nitrogenous bases adenine
• (A), guanine (G), cytosine (C), and
• thymine (T) in case of RNA uracil (U) is
• used instead of thymine (T) and the sugar
• is also different, ribose instead of
• deoxyribose.

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• DNA
• All living things have chromosomes
• inside the nuclei of their cells, the
• Chromosomes are made of DNA.
• The number and sequence of amino acids in a
  protein chain, determines the unique
  characteristics of that particular protein.
• The sequence of the nucleotides (or in other
  words the nucleotides bases) of a gene, is the
  determining factor that codes for the
  corresponding sequence of amino acids of that
  particular protein, this one gene is called one
  protein hypothesis.

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• DNA Structure

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• What is a nucleotide?

A nucleotide includes a sugar molecule, a
phosphate group, and a nitrogenous base bonded
together.
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• The Nitrogenous Bases
• Adenine Cytosine
• Guanine Thymine
• Uracil
• Purines
• (Double rings)
• Pyrimidines
• (Single rings)

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• The Nitrogenous Bases
• Are adenine (A), guanine (G), cytosine (C),
• and thiamine (T) in case of RNA uracil (U)
• is used instead of thiamine (T).
• The nitrogenous bases of the adjacent
• nucleotides are paired as follows
• A-T or T-A
• G-C or C-G
• Since there are 4 bases and each codon
• that codes for an amino acid is made of 3
• Bases, then there is a probability of 64
• Codes of base triplets (4364),which are
• more than enough to code for the 20
• available amino acids.