Assignment Biochemistry I (1)

Wan Muhamad Qusyairi Bin Wan Mazlan	AS1142B1
Diploma in Microbiology	BIOCHEMISTRY I

1.      Why only L-form amino acids are commonly found in protein?

      The L-form amino acids are more commonly found in protein because only L-form amino acid is manufactured in cells and incorporated into proteins.  The eukaryotes cells do not have the enzymes to synthesize the D-form amino acids.  The D-form amino acids are more commonly found in lower organisms in the cell walls of bacteria, but not in bacterial proteins.

2.      Why amino acid is important for babies?

      Because we normally ingest more protein (and thus amino acids) then we need, only a small % is used to make new protein.  For example, less than 5% of the amino acid phenylalanine is used even in a growing child and even less in a grown adult.  All the rest is burned as energy or converted to another amino acid called tyrosine and other amino acids important to the way the brain functions.  When an infant cannot burn an amino acid normally, several things happen:

• 1.  Excess is converted in the body to other compounds, many of which are toxic

• 2.  There can be a deficiency of some compounds which are made from that amino acid—often things important for brain function.

3.      What is the function of H₂O₂ in hair dyes?

      Basically, hydrogen peroxide is involved in a reaction to (apparently) eliminate melanin from hair, but how exactly does it do that? Well, it doesn’t really eliminate melanin, but in the presence of hydrogen peroxide, this pigment is oxidized and converted to a colourless compound.  Looking at it in more detail, hydrogen peroxide converts melanin’s double bonds into single bonds, blocking its ability to absorb light, thus effectively making it “disappear”. This reaction also releases sulphur, accounting for the characteristic odour of hair colour treatments. In this case, the natural yellowish colour of keratin comes through instead, effectively producing blonde hair. As eumelanin is attacked faster than phaeomelanin, some shades of red can still be visible after a short treatment with hydrogen peroxide. In contrast, if the treatment is too long, the result is a pure white hair, after both forms of melanin are completely oxidized.

Typically, hair lightening products are mixed in an alkaline solution, to make it easier for hydrogen peroxide to cut through the cuticle and reach the medulla, where melanin is stored. While any base could soften the cuticle, old hair product recipes relied on ammonia for this effect, as this compound could also break down small melanin particles, allowing easier access for the hydrogen peroxide. However, concerns about its harshness led to the development of alternative components and most modern products boast an ammonia-free content. Other ingredients may include persulphate salts to accelerate the reaction and multiple stabilizing chemicals to prevent the breakdown of hydrogen peroxide.

4.      What is the function of H₂O₂ inside our body antibacterial protecting?

      Hydrogen peroxide is generated in vivo by the dismutation of superoxide radical both non-enzymatically and catalyzed by superoxide dismutase enzymes. Hydrogen peroxide is also directly produced by a range of oxidase enzymes including glycollate and monoamine oxidases as well as by the peroxisome pathway for beta-oxidation of fatty acids. With the apparent exception of cardiac muscle, mitochondria in most tissues appear to have limited capacity to remove H₂O₂, in that they readily generate substantial amounts of H₂O₂ in vitro and probably in vivo. Although mitochondria contain glutathione peroxidase and thioredoxin-linked peroxidase activities, the efficiency of these enzymes in removing H₂O₂ is uncertain given the ease with which mitochondria release H₂O₂. It thus seems likely that most or all human cells are exposed to some level of H₂O₂, with the mitochondria being an important source. However, certain tissues may be exposed to higher H₂O₂ concentrations.

5.      What is the function of Fe³⁺ react with H₂O₂?

      A Fe3+ ion acts as a catalyst in the reaction.  In this reaction, it acts as a homogeneous catalyst in which the catalyst is in the same phase as the reaction mixture.  The Fe³⁺ ions will speed up the rate of reaction of hydrogen peroxide and lower the activation energy of the reaction.  The reaction will be like this :

Fe³⁺ + H₂O₂ + OH.           Fe³⁺ + HOO. + H₂O             Fe²⁺ + H⁺ + O₂ + H₂O

6.      What are the properties of enzymes?

      Enzymes are proteins that are biological catalysts

      They reduce the activation energy required for a reaction to occur and thus speed up a reaction

      Temperature, above a certain point (optimum temperature), causes them to break down and they are gradually destroyed (denaturing)

      They work best at a particular pH (optimum pH) and are once again destroyed by low or high pH's

      They have a specific shape, with one particular part, known as the active site, which is specific to the substrate they speed the reaction of. These means they are specific to one type of reaction.

      They aren't used in the reaction so they're re-usable.

7.      What is the characteristic of enzymes and how they bind?

      The characteristic of enzymes:

      Enzymes possess great catalytic power.

      Enzymes are highly specific.

      Enzymes show varying degree of specificities.

      Absolute specificity where the enzymes react specifically with only one substrate.

      Stereospecificity is where the enzymes can detect the different optical isomers and react to only one type of isomer.

      Reaction specific enzymes, these enzymes as the name suggests reacts to specific reactions only.

      Group-specific enzymes are those that catalyze a group of substances that contain specific substances.

      The enzyme activity can be controlled but the activity of the catalysts cannot be controlled.

      All enzymes are proteins.

      Like the proteins, enzymes can be coagulated by alcohol, heat, concentrated acids and alkaline reagents.

      At higher temperatures, the rate of the reaction is faster.

      The rate of the reaction involving an enzyme is high at the optimum temperature.

      Enzymes have an optimum pH range within which the enzymes function is at its peak.

      If the substrate shows deviations larger than the optimum temperature or pH, required by the enzyme to work, the enzymes do not function such conditions.

      Increase in the concentration of the reactants, and substrate the rate of the reaction increase until the enzyme will become saturated with the substrate; increase in the amount of enzyme increases the rate of the reaction.

      Inorganic substances known as activators increase the activity of the enzyme.

      Inhibitors are substances that decrease the activity of the enzyme or inactivate it.

      Competitive inhibitors are substances that reversibly bind to the active site of the enzyme, hence blocking the substrate from binding to the enzyme.

      In competitive inhibitors are substances that bind to any site of the enzyme other than the active site, making the enzyme less active or inactive.

      Irreversible inhibitors are substances that form bonds with enzymes making them inactive.  

             how they bind

      Complementarity: Molecular recognition depends on the tertiary structure of the enzyme which creates unique microenvironments in the active/binding sites. These specialized microenvironments contribute to binding site catalysis.

      Flexibility: Tertiary structure allows proteins to adapt to their ligands (induced fit) and is essential for the vast diversity of biochemical functions (degrees of flexibility varies by function)

      Surfaces: Binding sites can be concave, convex, or flat. For small ligands – clefts, pockets, or cavities. Catalytic sites are often at domain and subunit interfaces.

      Non-Covalent Forces: Non-covalent forces are also characteristic properties of binding sites. Such characteristics are: higher than average amounts of the exposed hydrophobic surface, (small molecules – partly concave and hydrophobic), and displacement of water can drive binding events.

      Affinity: Binding ability of the enzyme to the substrate (can be graphed as partial pressure increases of the substrate against the affinity increases (0 to 1.0); the affinity of binding of protein and ligand is a chemical attractive force between the protein and ligand.