IB Chemistry Option B 2 Biochemistry.pptx

IB Chemistry Option B 2 Biochemistry

1. Biochemistry HL only IB CHEMISTRY: OPTION B SL & HL

2. B.2 Proteins and enzymes

3. B.2 Proteins and enzymes

4. Amino acids are the monomers or building blocks of proteins (polymers) Each amino acid contains an (-NH 2 ) amino group and a (-COOH) carboxyl group Amino acids 2 α “2-aminoacid or α - aminoacid ”

5. Among 500 aminoacids only 20 can combine to form proteins: proteinogenic (see data booklet) which vary with the R side chain Amino acids Isoelectric point ( pI ) is the pH of a solution at which the net charge of a protein becomes zero . If a solution’s pH is above pI , the Surface of the protein is negatively charged and  therefore molecules will exhibit repulsive forces.

6. Our body needs 20 different amino acids to grow and function properly. Though all 20 of these are important for your health, only  nine  amino acids are classified as essential  Amino acids Information about aminoacids , names , formulae and isoelectric points can be found in the DATA BOOKLET Our body does not produce thtem . We have to ingest them Our body produces them

7. In neutral solutions both groups exist as ions . One proton from the -COOH migrates to the –NH 2 group . Amino acids are amphoteric meaning they can act as both acids and bases (weak acid&base groups) HCl ----- H+ + Cl- // NaOH ----Na+ + OH- Amino acids will act as buffers by absorbing excess H + or OH - ions. Each amino acid has a pH in which it is electrically neutral called the isoelectric point . When the pH is below this it will be a positive ion, above this and it will be a negative ion. Buffers are solutions that keep the pH constant Amino acids’ properties Net charge =0

8. The NH 3 + group in the zwitterion is the acidic center that can lose a H + when combined with a strong base, forming the anionic form . The –COO - group in the zwitterion is the basic center that can accept a H + when combined with a strong acid , forming the cationic form . Amino acids as zwitterions

9. At pH 6, aa with neutral R exists as zwitterions (net charge =0) The presence of an extra –COOH group in R, lowers the pI to 2.8-3.2( ) The presence of an extra NH2 groups increase the pl to 7.6-10-8 ( ) Amino acids as zwitterions

10. Formation of a Protein When –COOH of one aa. Reacts with –NH2 of another aa a dipeptide is formed . The bond is known as: Peptide linkage /bond or amide linkage / amide bond. This is a condensation reaction Read how to name peptides on pg 555 (Oxford)

11. Serine Valine Tyrosine Cysteine A Short Polypeptide Peptide Bond Formation of a Protein 3 H 2 O

12. Primary structure The amino acid sequence of the protein (intramolecular forces). Covalent (amide peptide) bonding. Secondary structure This is due to regular repeating hydrogen bonding along the same peptide chain and may consist of turns known as α –helix , or sheets known as β –pleated sheets . Tertiary structure This is due to the R side groups (note these are called intramolecular forces) These groups not only influence the isoelectric point but also include hydrophobic/hydrophilic groups, hydrogen bonding, ionic bonds between charged side groups, and disulfide bridges (covalent and strongest of all these linkages) Denaturing of the protein is said to occur at this level Quaternary structure The relationship of the polypeptide to other polypeptides (proteins such as hemoglobin are actually four interlinking polypeptides) Protein structure Find more info about protein structure in Oxford pgs 556-559

13. Fibrous vs Globular proteins Protein Type Role Function Keratin Fibrous Structure Protective covering for hair, wool, claws Collagen Fibrous Structure Connective tissue of skin and tendons Polymerase Globular Enzyme Catalyzes DNA synthesis Insulin Globular Communication Hormone for glucose homeostasis Hemoglobin Globular Transport O 2 transport Antibodies Globular Immune system Protect ion from pathogens Fibrous proteins – insoluble structural components that are elongated with a dominant secondary structure Globular proteins – soluble functional tools that have a spherical shape and a dominant tertiary structure

14. By using hydrolysis, proteins can be broken up into their constituent amino acids Hydrolysis uses enzymes, or heat/acid Amino acids can then be detected by either chromatography or electrophoresis Protein analysis

15. Amino acids will move at different rates depending on their solubility with the solvent and molecular size Amino acids are made visible by spraying with a locating reagent ( ninhydrin ). Each amino acid will have a special R f value (Retention factor). R f =   1. Chromatography

16. IB QUESTION :

17. ANSWER:

18. Amino acids are placed in a pH buffer solution An electric current is then passed through Amino acids will move at different rates depending on their isoelectric point Detection is made by staining, or by fluorescing under UV light 2. Electrophoresis

19. IB QUESTION : From the data booklet

20. ANSWER : Describe intermolecular forces in aminoacids . Find the answer on pg 554 (Oxford)

21. Enzymes - action Organic molecules (proteins) that increase reaction rates faster than inorganic catalysts by binding substrate to a specific active site Sensitive to temperature and pH, heavy metal ions can also denature the proteins Can be very specific (and vary in their specificity) determined by there tertiary and quaternary shape Some proteins require co-factors to bind to them for activity Organic co-factors such as vitamins are also called co-enzymes Inorganic co-factors include metal ions Animation of enzyme specificity Animation of induced fit model

22. Enzymes – organic vs inorganic Enzyme Proteins (except ribosomes) Highly specific Maximum rate with substrate saturation Homogenous (in aq state) Regulated by inhibitors and activators Work within narrow limits Increase rates by 1000 to 1000 000 Inorganic catalyst Metal ions or complex molecules Much less specific Do not show saturation Homogenous and heterogenous Not regulated Work at high temp and pressure Relatively small increase in rate compared to enzymes

23. Enzymes – effect of temperature and pH Temperature: Initial increase in rate due to increase in temperature as any normal reaction. Sudden decrease in rate due to the disruption of hydrogen bonds and other forces holding the tertiary structure (Denaturation) pH: Reactions with the R-groups and H ion concentrations change the tertiary structure

24. Enzymes – effect of heavy metal ions Heavy metal ions: Pb, Cu, Hg, Ag react with sulfhydryl groups –SH forming covalent bonds which many change the tertiary structure

25. Answer