BIO MOLECULES Pt 3 (Proteins)

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BIO MOLECULES Pt 3 (Proteins)
2012-03-31 13:27:37
biology bio molecules unit

Part 3 - mostly on proteins and amino acids etc
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  1. What elements are proteins made out of? How many percent of organic matter in cells does it make up?
    • Carbon, hydrogen, oxygen & nitrogen. (some proteins also contain sulfur)
    • 50% of organic matter in cells (proteins)
  2. List the functions of proteins. (5)
    • Structural components - eg. muscle and bone
    • Membrane carriers and pores (provide transport across membranes) - eg. for active transport and facilitated diffusion.
    • All enzymes are proteins
    • Many hormones
    • Antibodies
    • (Overall, proteins provide building material important for growth and repair in all organisms. Also crucial to most metabolic activity)
  3. All amino acids have the same basic structure. What is the parts of the amino acid called?
    • All have amino group at one end of the molecule
    • An acid group at the other end of molecule
    • And a carbon in between.
  4. How many types of naturally occuring amino acids are there?
  5. Amino acids are joined ___-__-___ to give a repeating "_______".
    • Amino acids are joined end-to-end to give a repeating "backbone".
    • NCCNCCNCC...
  6. Imagine the structure of an amino acid.
  7. What can the R-group be?
    • In glycine it is a hydrogen atom (simplest amino acid)
    • Some R groups are large - larger than CNN part of molecue.
    • Some are positively charged, others negatively, some are hydrophobic, some are hydrophilic.
  8. What are essential amino acids?
    Around 8-10 types of the amino acids that cannot build from material they take into their bodies, and thus are essential part of the diet. (Most of these are found in meat)
  9. Animals cannot ____ excess amino acids. In what process are amino groups removed? And where in mammals does this take place? And why is it necessary?
    • Cannot store
    • Process called deamination
    • Takes place in the liver - amino groups converted into urea and removed in urine.
    • Because the amino groups makes them toxic if too much is present.
  10. What is the name of the covalent bond formed between two amino acids? What is the new molecule called? Condensation reaction happen between which parts?
    • Peptide bond
    • New molecule called dipeptide
    • The condensation reactions happen between the acid group of one amino acid and the amino group of another.
  11. Why are some amino acids in a polypeptide chain sometimes referred to as amino acid residues?
    Because part of the molecule is lost during condensation reaction that produces the peptide bond.
  12. A protein may consist of a _____ polypeptide chain of hundreds of amino acids, or it can consist of _____ ____ ___ polypeptide chain to form an even larger molecule.
    • single
    • more than one
  13. Where are proteins made and what is this process called?
    • On ribosomes
    • Called protein synthesis
    • Uses information in the form of a molecule called messenger RNA
  14. The function of each protein is determined by what? And what is primary structure?
    • Function of protein determined by its structure.
    • The unique sequence of amino acids of a polypeptide or protein is called its primary structure.
  15. What is the name of enzymes that catalyse the breaking of peptide bonds?
    Protease enzymes
  16. Give an example of when/where peptide bonds are broken other than during digestion in the stomach.
    Hormone regulation - target cells for a specific hormone will have enzymes that can break down that hormone, so that its effects are not permanent.
  17. Examiner's tip!
    Always state that condensation or hydrolysis reactions are enzyme-catalysed reactions if you are referring to the process within organisms.
  18. Give 2 descriptive words to describe how polypeptide chains are shaped.
    • Coiled up or pleated
    • These coils and pleats are held in place by numerous hydrogen bonds.
    • Amount depends upon amino acids, so depends on the primary structure.
  19. Describe secondary structure of proteins.
    • Formed when chain of amino acids coils or folds to form an alpha helix or a beta pleated sheet.
    • Hydrogen bonds hold the coils in place.
  20. What is tertiary structure?
    Refers to the overall 3D structure of the final polypeptide or protein molecule.
  21. Give 3 examples of how tertiary structure is vital to the function of proteins.
    • Hormones need to be a specific shape to fit into the hormone receptor.
    • Enzymes need to have an active site which is complementary in shape to that of its substrate.
    • Structural proteins such as collagen is shaped to be strong by protein chains being wound around each other in specific way.
  22. Tertiary structure in proteins is stabilised by which bonds? Plus what other thing determines structure?
    • Disulfide bonds: (eg 2 cysteine amino acids)
    • Ionic bonds: some R groups carry a charge and therefore opposite charged groups
    • Hydrogen bonds: slightly negative and positive (like in secondary structure).
    • Hydrophobic and hydrophilic interactions
  23. What happens if you heat a protein too much?
    • The increased kinetic energy causes the molecules to vibrate and breaks some of the bonds holding tertiary structure in place.
    • The protein denatures.
  24. What are the two main types of 3D shapes of proteins?
    • Globular proteins - roll up into ball-shaped structure. Any hydrophobic R-groups turned inwards towards centre, and any hydrophilic R-groups are outside. (makes it insoluble). Usually have metabolic roles. eg. enzymes
    • Fibrous proteins - form fibres. Most have regular, repetitive sequences of amino acids. Usually insoluble in water. Usually structural roles. eg. keratin & cartilage
  25. Proteins which have a quaternary structure have what?
    • Made up of more than one polypeptide subunit joined together, or a polypeptide and an inorganic component. They will only function if all the subunits are present.
    • eg. haemoglobin & collagen (need to know about them) and insulin.
  26. What are prosthetic groups?
    • Groups in a protein that are not made of amino acids but are still essential part of the molecule.
    • eg. haem group of haemoglobin (need to know)
  27. What is the haem group?
    The specialised part of each polypeptide in a haemoglobin molecule which contains an iron (Fe^2) ion. The oxygen molecule binds to the iron ion in the haem group, and this is responsible for the red colour of blood.
  28. Describe some of the features of haemoglobin.
    • Globular protein
    • Soluble in water (hydrophilic region on outside)
    • Wide range of amino acids in primary structure (give specific interactions to form tertiary structure which is vital)
    • Contains prosthetic group - haem group
    • Much of molecule is wound into alpha helix structures
  29. What is a collagen molecule made up of?
    • Three polypeptide chains wound around each other.
    • Hydrogen bonds between chains
  30. What is a collagen fibril made up of?
    Collagen molecules forming covalent bonds called cross-links staggered along molecule.
  31. Give 3 examples of how collagen is used to provide mechanical strength.
    • Walls of arteries (prevents high pressure from bursting the walls)
    • Tendons
    • Bones - reinforced with materials such as calcium phosphate
    • Cosmetic treatments
  32. Features of collagen that can be compared with haemoglobin.
    • Fibrous protein
    • Insoluble in water
    • Approx 35% of primary structure is one type of amino acid (glycine)
    • Does not have a prosthetic group
    • Much of molecule consists of left-handed helix structures.