Protein Structure

• Polypeptide Chain

  • A polypeptide chain is the combination of amino acids that are connected together by peptide bonds.
  • Poly = many. Peptide = proteins.
• Proteins

  • Proteins are large macromolecules that are constructed from the 20 amino acids. The amino acids are bound together by peptide bonds.
  • Proteins are made up of varying combinations of the 20 amino acids.
  • this means different proteins can vary in the number, type, and sequence of amino acids, providing unique proteins.
• Proteins

  • Proteins are dynamic and are continually changing, examples are by binding to receptors on cell membranes, forming complexes with other molecules, being synthesised and broken down.
  • The unique shape of each protein determines the specific function of the protein.
• Uses of Proteins

  • Provide structure to cells and the body: hair, nail, skin and muscles are all made up of proteins.
  • Cellular communication; hormones such as insulin are proteins, and receptor proteins.
  • Protecting the body: antibodies which help fight disease.
  • Catalysing (speeding up) reactions: enzymes
  • Channel proteins: e.g. absorb glucose through the small intestine. Let passage of substances through cell membrane.
• Protein Structure

  Protein structures are broken down into:

  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
• Primary Structure

  • Primary structure of proteins refers to the linear sequence of amino acids.
  • Amino acids are held together by peptide bonds.
• Secondary Structure

  • Secondary structure of proteins refers to coiling and folding of the protein.
  • Attraction between amino acids is due to hydrogen bonding.
  • Two most common shapes are alpha helix (coiling) and beta pleated sheets (folding).
• Tertiary Structure

  • Tertiary structure refers to the 3D shape of the polypeptide (based on the way it’s folded).
  • Tertiary structure occurs due to forces of attraction between specific amino acids in the polypeptide chain.
  • These include hydrogen bonds, but stronger ionic bonds and covalent disulfide bonds.
  • 3D shape with unique folds, groove and clefts gives different function of proteins – therefore 3D structure is crucial.
• Quaternary Structure

  • Quaternary structure refers to the combination of multiple different polypeptide chains (strings of amino acids).
  • These form by the polypeptides chemically bonding together.
• Functional Proteins

  Some of the types of proteins:

  • Enzymes – increase rate of reactions.
  • Receptor proteins and peptide/protein hormones – assist with chemical messages around the body.
  • Antibodies – assist with body defence against infectious diseases.
  • Regulatory proteins – turn genes “on & off”, allowing for genes to be read or not.
• Proteomics

  • Proteome is a term used to refer to all proteins within a cell or organism.
  • Proteomics is the study of proteins and the abundance, variation and modification of proteins.
  • Biomarkers are molecules, such as proteins, and often give indication of abnormal processes or diseases due to proteins.
• Describe what it means to say that protein structure is linked to the function of that protein.

  Each protein molecule has its own 3D structure, the structure is intrinsically linked to the function of that protein. An example would be the protein insulin that has a 3D shape complementary to a membrane receptor on several cells e.g. liver cells. When it binds to these receptors it initiates a response by the cell.
• Briefly outline the main factors that determine the primary, secondary, tertiary, and quaternary structure of proteins.

  Primary Structure

  • The determining factor is the number, sequence, and type of amino acids in the primary structure.

  Secondary Structure

  • Because of original make up, hydrogen bonds form between amino acids forming alpha helices or beta pleated sheets secondary structure.
• Briefly outline the main factors that determine the primary, secondary, tertiary, and quaternary structure of proteins.

  Tertiary Structure

  • Forms spontaneously due to multiple forces of reactions between amino acids giving the protein its unique 3D structure.

  Quaternary Structure

  • Not all proteins have a quaternary structure, arises when a protein is made up of more than one polypeptide chain.
• Describe why some proteins do not have a quaternary structure

  Not all proteins have a quaternary structure, as they may consist of only one polypeptide chain.
• Haemoglobin is a protein molecule that consists of 4 polypeptide chains; 2 alpha and 2 beta chains.

  How many gene are required to code for two molecules of haemoglobin?

  Two genes code for haemoglobin, one for the alpha chain and one for the beta chain.
• Haemoglobin is a protein molecule that consists of 4 polypeptide chains; 2 alpha and 2 beta chains.

  Describe what is required to form the quaternary structure of this molecule.

  Two alpha and two beta chains have to be synthesised at the ribosome and the four polypeptide chains are arranged together to form one protein molecule of haemoglobin.
• Explain how it is possible for each different protein molecule to have a unique primary structure.

  The primary structure is determined by the number, type, and sequence of amino acids. Each protein differs in regard to each of these 3 factors.
• Describe how it is possible for a cell to make hundreds of thousands of different protein using only 20 amino acids.

  As proteins differ in their number, type, and sequence of amino acids, there is an infinite number of possible proteins that can be made by changing these three variables.
• State four functions of proteins in cells and give an example of each.

  • structural proteins (keratin in skin)
  • enzymes (peptin)
  • hormones (insulin)
  • antibodies (against HIV virus)
• Explain how it is possible for the estimated 21,000 genes in the human genome to code for over 250,000 different protein molecules. 


  This variation is due to the fact that it is an oversimplification to say that one gene is transcribed and translated into one polypeptide or protein. Processes, such as alternative splicing introduces variation through exons being spliced out of pre-mRNA in various ways, resulting in many possible mature mRNA's from one gene. Therefore, many possible proteins can be produced from one gene.
• Explain how the different shapes and chemical properties of hormones enable these molecules to control metabolic pathways.

  The specific shape of a particular hormone is complementary to one specific surface cell receptor embedded into a particular type of a cell's plasma membrane. When this binding occurs, it initiates a specific response inside the cell, such as gene expression of enzymes involved in the control of metabolic pathways.
• Adrenaline is a hormone that binds to receptor proteins in the cell membrane of target cells. This binding causes glycogen stored in the cells to be broken down to form glucose. Explain why adrenaline can act on liver cells and not all cells in the organism.

  Only cells that possess the specific cell membrane receptor that can bind in a complementary fashion to adrenaline will respond, such as liver cells.
• Foreign substances, such as poisons that have been ingested or surface molecules on bacteria and viruses, are called antigens. Detection of antigens in a human simulates lymphocyte cells to release antibodies. Explain how antibodies inactivate invaders, such as bacteria and viruses.

  Invaders such as bacteria and viruses are characterised by specific antigens or antigenic markers on their membranes. The antibodies made by the body are complementary to the antigens and bind to the bacteria and viruses. This action can assist in a number of ways in the destruction of these invaders.
• Describe the importance of the primary structure in determining the pleated sheet

  It is the binding between the specific amino acids in the primary structure that leads to the secondary structure e.g. a pleated sheet
• Explain how this secondary structure is important for the function of the lysozyme enzyme

  The secondary structure of a protein forms localised 3D structures called beta pleated sheets (and alpha helices). Lysozymes will have specific numbers and types of alpha helices and beta sheets based in its unique primary structure. Ultimately, the secondary structure will help determine the final 3D shape of the protein. A lysozyme will have a specific active site that enables it to break down cells walls in bacteria.
• All cells have the same DNA but are capable of producing different types of protein molecules.

  Different cells have different genes that are switches on and off. Not all genes are active in all cells.
• The same cell produces different proteins at different times.

  Gene activity is carefully controlled. There are a range of triggers that determine what proteins are made at a specific time e.g. high sugar levels in blood trigger insulin production.
• A->B->C->D

  Suggest how the final product might act as a repressor protein on a gene to stop the production of molecule A

  D will have a specific 3D shape. If D was to bind to a promoter region near a gene involved in the production of A, it may stop transcription of that gene.

  • Predict how this might be an advantage to the cell in which this interaction occurs.

  This would mean that when ample amounts of D are available, the cell can slow or stop the production of A. This will conserve energy and reduce overproduction of D.