Proteins

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Proteins

• Topic 2.4
• IBHL Biology

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Introduction

• Proteins are a very important biological
  molecules that are involved in almost every
  activity that organisms do.
• They comprise more than 50 of the dry mass in
  most cells.
• They are involved in chemical reactions,
  structures, transport, cell to cell
  communication, movement, and immunity.
• They are also the structural component of
  enzymes.
• Proteins are constructed from polymers of amino
  acids and are referred to as polypeptides. They
  are held together by peptide bonds.

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2.4 U1 Amino acids are linked together by
condensation to form polypeptides.

• Amino acids are the sub units of proteins and
  they bond together to form polypeptides.
• There are 20 different amino acids and they are
  distinguished by their R-group but they all have
  the same generalized structure.

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Condensation of Amino Acids

• Condensation reactions can join two amino acids
  together to form dipeptides or many amino acids
  together to form large chains called polypeptides
  (proteins).
• As each bond (peptide bond) is formed a molecule
  of water is produced.
• This process is performed by ribosomes in a
  process known as translation.

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2.4 S1 Drawing molecular diagrams to show the
formation of a peptide bond

• Draw the formation of a peptide bond in your
  sketch book.

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2.4 A2 There are 20 different amino acids in
polypeptides synthesized on ribosomes

• There are 20 different amino acids used to build
  thousands of different proteins. The amino acids
  are distinguished from one another by their R
  group also known as a side chain.
• The amino acids can be grouped according to the
  properties of their side chains. There are polar
  amino acids, non-polar amino acids and
  electrically charged amino acids.

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20 Different Amino Acids

• You do not need to know the names of the 20
  different amino acids however you should know
  that organisms can arrange them in polypeptides
  to produce thousands of different proteins.
• Also, some amino acids can have variations in
  their structure which changes their
  characteristics.
• For example, a modified version of the amino acid
  proline known as hydroxyproline is found in the
  protein collage. It gives collagen, a structural
  protein found in ligaments, tendons, skin and
  blood vessels, more stability.

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2.4 U3 Amino acids can be linked together in
any sequence giving a huge range of possible
polypeptides.

• The possibilities of amino acid sequences are
  huge.
• Polypeptides contain amino acid numbers ranging
  from 20 to tens of thousands.
• This table identifies the infinite possibilities
  for polypeptide sequences.

of amino acids Number of possible amino acid sequences Number of possible amino acid sequences
1 201 20
2 202 400
3 203 8 000
4 204 160 000
5 205 3 200 000
6 206 64 000 000
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2.4 U4 The amino acid sequence is coded for by
genes

• The information needed to produce proteins is
  stored in DNA. It is coded for by genes that
  contain three base pairs per amino acid. The
  sequence of base pairs controls the building of
  polypeptides during translation. We will cover
  this in detail in unit 5.

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2.4 U5 - A protein may consist of a single
polypeptide or more than one polypeptide linked
together

• Some polypeptides are two or more strands linked
  together. Integrin is an example of a protein
  that has two separate polypeptides that work
  together to make connections between structures
  that are inside
  and outside
  of cells.

• Some polypeptides are a single polypeptide such
  as lysozyme.
• It is an enzymes secreted in nasal mucus and
  tears that kills bacteria by digesting their cell
  walls.

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2.4 U5 - A protein may consist of a single
polypeptide or more than one polypeptide linked
together

• Hemoglobin is composed of 4 polypeptides along
  with a non-polypeptide group known as a heme
  group.
• This protein transports
  o oxygen in the blood.

• Collagen is composed of three polypeptides. It
  is a structural protein.

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2.4 U6 The amino acid sequence determines the
three dimensional conformation of a protein

• The conformation of a protein refers to its three
  dimensional shape. There are 4 levels of protein
  structure and the level it conforms to is
  dependent on its amino acid structure. (see
  handout)
• Proteins are often described as being globular or
  fibrous. The sequence of amino acids determines
  the shape of the protein.
• Fibrous proteins have a structural role and
  globular proteins have functional roles in a
  cells metabolism.

http//www.youtube.com/watch?vyZ2aY5lxEGE
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Fibrous Proteins

• Fibrous proteins have a long and narrow shape and
  are mostly insoluble in water.
• They are composed of many polypeptide chains
  organized into a long, narrow shape.
• Some examples are collagen, a protein that plays
  a structural role in human connective tissues and
  actin, a protein found in muscle which plays a
  role in muscular contractions.

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Globular Proteins

• Globular proteins have a rounded shape (three
  dimensional) and they are mostly soluble in
  water.
• Hemoglobin is an example of a globular protein
  and it is involved in delivering oxygen to body
  tissues.
• Insulin is another example of a globular protein
  and it plays a role in regulating blood glucose
  levels in humans.

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2.4 U7 Living organisms synthesize many
different proteins with a wide range of functions.

• Organisms synthesize thousands of different
  proteins in their cells and each protein is
  different. They have different sequences of
  amino acids and as mentioned earlier, that
  sequence determines the shape of the protein and
  the shape determines the function.
• Refer to the handout mentioned earlier for a
  summary of the functions and variety of proteins.

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Use the following terms to complete the chart on
your handout

• Muscle contraction
• Membrane transport
• Hormones
• Cytoskeletons
• Tensile strengthening
• Cell adhesion

• Immunity
• Blood clotting
• Receptors
• Catalysis
• Packing of DNA
• Transport of nutrients gases

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2.4 A1 Rubisco, insulin, immunoglobulins,
rhodopsin, collagen and spider silk as examples
of the range of protein functions.

• Refer to handout and chart completed in class.

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2.4 U8 Every individual has a unique proteome.

• A proteome is defined as all the proteins
  produced by a cell, a tissue or an organism.
• We can use a process known as gel electrophoresis
  to extract proteins from samples and determine
  how they are being produced. Antibodies with
  fluorescent markers are used to identify the
  proteins.
• Proteomes are variable from cell to cell due to
  the fact that cells differ in their functions and
  activities.
• While there are many similarities within species,
  individuals still have many variations within
  their proteomes which can be due to small
  differences in the amino acid sequences of
  proteins.

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2.4 A2 Denaturation of proteins with a wide
range of functions.

• The three dimensional structure of proteins is
  maintained or stabilized by bonds or interactions
  between the R-groups of amino acids. These
  bonds or interactions are weak and can be broken
  or disrupted fairly easily.
• When this occurs it cause a change in the
  conformation of the protein and this is known as
  denaturation.
• When a protein is denatured it changes shape and
  these changes can be temporary or permanent. Two
  factors than can denature proteins are heat and
  pH.

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2.4 A2 Denaturation of proteins with a wide
range of functions.

• Extreme changes in pH can cause proteins to
  denature. It causes changes in the charges on R
  groups which breaks the bonds or causes new bonds
  to form. This will alter the structure of the
  protein. Some proteins are exceptions such as the
  stomach enzyme pepsin (pH 1.5)

• Heat can denature proteins because it causes
  vibrations in the molecule that breaks bonds.
• Proteins vary in their tolerance of heat and can
  cause temporary or permanent changes.