WATER, SOLUTION AND BUFFER

SECOND - PAPER TASK

 

WATER, SOLUTION AND BUFFER

Referensi;

1.       Biochemical Calculation

2.       Biochemistry & Genetics - Pretest Self-Assessment & Review 

Tugas .

Selesaikan problem dibawah

a.       Berapa gram NaOH(s) yang dibutuhkan untuk membuat 250 mL larutan 0,04 M. Tentukan konsentrasi dari larutan ini dalam satuan N, g/Liter, mg% dan osmolaritas.

b.      Berapa mL 4 M H₂SO₄ yang dibutuhkan untuk membuat  2 L  larutan H₂SO₄  0,002 M.

c.       Tentukan kekuatan ion (ionic strength) dari 0.03M larutan Fe₂(SO₄)₃

d.      Saudara diberi HCl pekat (28% b/b), Specific gravity =1.15). Buatlah 2 Liter larutan 0,5 M HCl dari HClpekat yang saudara punyai.

e.      Hitung 1. Molalitas dari HCl pekat (28% b/b), Specific gravity =1.15), 2. Hitung fraksi mol didalam larutan.

f.        Spesifik volume dari amonimum sulfat  (solid) adalah 0,565 mL/g. Kelarutan ammonium sulfat pada 0⁰C adalah 706 g/1000g air. Hitung (a) konsentrasi ammonium sulfat didalam larutan jenuh pada 0⁰C dan (b) jumlah ammonium sulfat yang harus ditambahkan pada 0⁰C kedalam 750 mL dari larutan  “40%-jenuh” untuk membuat nya 60%-jenuh).

g.       Berapa mililiter dari larutan ammonium sulfat jenuh yang harus ditambahkan kedalam 40 mL larutan 25% jenuh untuk membuat larutan 70% jenuh?. Dianggap bahwa volumenya bertambah.   

107. Water, which constitutes 70% of body weight, may be said to be the “cell solvent.” Which of the following properties of water most contributes to its ability to dissolve compounds? a. Strong covalent bond formed between water and salts

b. Hydrogen bond formed between water and biochemical molecules

c. Hydrophobic bond formed between water and long-chain fatty acids

d. Absence of interacting forces

e. Fact that the freezing point of water is much lower than body temperature

97. A solution of acid is prepared for cleaning surgical instruments by

adding 0.5 L of 2 mM hydrochloric acid (HCl) to 0.5 L of pure water,

which has a hydrogen ion concentration of 10−7 M. The initial pH of the

pure water, then the pH after adding the HCl, are

a. 7, then 3

b. 7, then 4

c. 7, then 1

d. 14, then 3

e. 14, then 4

98. The greatest buffering capacity at physiologic pH would be provided

by a protein rich in which of the following amino acids?

a. Lysine

b. Histidine

c. Aspartic acid

d. Valine

e. Leucine

99. The relationship between the ratio of acid to base in a solution and its

pH is described by the Henderson-Hasselbalch equation

pH = pK + log [base]/[acid]

The pK of acetic acid is 4.8. What is the approximate pH of an acetate solution

containing 0.2 M acetic acid and 2 M acetate ion?

a. 0.48

b. 4.8

c. 5.8

d. 6.8

e. 10.8

100. Since the pK values for aspartic acid are 2.0, 3.9, and 10.0, it follows

that the isoelectric point (pI ) is

a. 3.0

b. 3.9

c. 5.9

d. 6.0

e. 7.0

101. A 0.22 M solution of lactic acid (pKa 3.9) is found to contain 0.20 M

in the dissociated form and 0.02 M undissociated. What is the pH of the

solution?

a. 2.9

b. 3.3

c. 3.9

d. 4.9

e. 5.4

102. Which of the combinations of laboratory results below indicates compensated metabolic alkalosis?

a. Low PCO2, normal bicarbonate, high pH

b. Low PCO2, low bicarbonate, low pH

c. Normal PCO2, low bicarbonate, low pH

d. High PCO2, normal bicarbonate, low pH

e. High PCO2, high bicarbonate, high pH

103. The graph below shows a titration curve of a common biochemical

compound. Which of the following statements about the graph is true?

a. The compound has one ionizable function

b. The compound has three ionizable side chains

c. The maximum buffering capacity of the compound is represented by points A

and B on the graph

d. Point A could represent the range of ionization of an amino function

e. Points A and B represent the respective pKs of á and side chain carboxyl groups

104. The pH of body fluids is stabilized by buffer systems. Which of the

following compounds is the most effective buffer at physiologic pH?

a. Na2HPO4, pKa5 12.32

b. NH4OH, pKa5 9.24

c. NaH2PO4, pKa5 7.21

d. CH3CO2H, pKa5 4.74

e. Citric acid, pKa5 3.09

105. Water, which constitutes 70% of body weight, may be said to be the

“cell solvent.” The property of water that most contributes to its ability to

dissolve compounds is the

a. Strong covalent bond formed between water and salts

b. Hydrogen bond formed between water and biochemical molecules

c. Hydrophobic bond formed between water and long-chain fatty acids

d. Absence of interacting forces

e. Fact that the freezing point of water is much lower than body temperature

 

 

Buffers and Buffering Capacity

A buffer is a partially neutralised acid which resists changes in pH. Salts such as Sodium Citrate or Sodium Lactate are normally used to partially neutralise the acid. Different combinations of acids and salts can be used as buffers, for example, Malic Acid with Sodium Lactate.

Buffers reduce the variation in the pH of an end-product, as shown on the graph at right. pH variation is detrimental to consistent quality.

Why use buffers? Buffers are used specifically to:

·         Reduce flavour variation from two pH effects:

·                     changes in flavour intensity of flavour chemicals with pH

·                     changes in sourness, sweet/sour balance with pH.

·         Decrease variation in colour shade of natural colours

·         Control gelling in pectin-based products

·         Reduce variation in texture from lot to lot

Buffering Capacity is the ability of the buffer to resist changes in pH

·         Buffering Capacity increases as the molar concentration (molarity) of the buffer salt/acid solution increases

·         The closer the buffered pH is to the pKa, the greater the Buffering Capacity

·         Buffering Capacity is expressed as the molarity of Sodium Hydroxide required to increase pH by 1.0

As shown by the graph, Acidulants: Buffering Capacity vs. pH, on the following page, the acidulants with higher molarity like Acetic Acid have a greater buffering capacity.The pKa of the acidulant is the other factor involved. As shown, the closer the buffered pH is to the pKa of the acid, the higher the buffering capacity. We can see that Acetic and Lactic Acids have narrower working ranges than the other acidulants. This is because they are monoprotic acids and therefore the pH range for dissociation is narrower than in the case of polyprotic acids like Malic or Fumaric Acids.

The effect of pH on enzyme actvity

The pH of a solution can have several effects of the structure and activity of enzymes.

For example, pH can have an effect of the state of ionization of acidic or basic amino acids. Acidic amino acids have carboxyl functional groups in their side chains. Basic amino acids have amine functional groups in their side chains. If the state of ionization of amino acids in a protein is altered then the ionic bonds that help to determine the 3-D shape of the protein can be altered. This can lead to altered protein recognition or an enzyme might become inactive.

Changes in pH may not only affect the shape of an enzyme but it may also change the shape or charge properties of the substrate so that either the substrate connot bind to the active site or it cannot undergo catalysis.

In geneal enzyme have a pH optimum. However the optimum is not the same for each enzyme.

For example in the figure below is represented a situation inwhich two different enzymes might have very different pH optima. The one depicted by the green curve might represent the pH optimum for the enzyme pepsin which degraded proteins (protease) in the vert acidic lumen of the stomach. The second curve (in red) might represent the enzyme carbonic anhydrase that works in the neutral pH of your cytosol.

source :

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/ph_def.htm

Enzyme Activity

        An enzymatic reaction is the conversion of one molecule into another; a chemical reaction catalyzed at the reactive sites on the enzyme. Considering the complex nature of the enzyme itself, it is not unreasonable to expect that many parameters will affect the rate of this catalytic activity. Enzyme activity can be influenced by:

• Spacing (steric hindrance)
• pH
• Temperature
• Substrate Concentration   (Michaelis-Menten Kinetics)

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Spacing

        Any groups that separate the enzyme from the support (or backbone) are referred to as spacing groups.  For an enzyme only one spacing group away, it would be very difficult for a substrate to find the active site. The backbone interferes sterically. But with more than one CH₂ (or other spacing groups), the enzyme can whip around and twist so that the active site is much more accessible. Usually, spacers that provide as much distance as six CH₂ groups are enough.
  

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Effect of pH Change

        Since enzymes are proteins, they are very sensitive to changes in pH.  Each enzyme has its own optimum range for pH where it will be most active.  This is the result of the effect of pH on a combination of factors: (1) the binding of the enzyme to substrate, (2) the catalytic activity of the enzyme, (3) the ionization of the substrate, and (4) the variation of protein structure.  The initial rates for many enzymatic reactions exhibit bell-shaped curves as a function of pH as shown in the example below.  (Note that this particular enzyme is most active at a pH of zero, but this is not the case for all.)

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Effect of Temperature Change

        As temperature increases, the rate of reaction also increases, as is observed in many chemical reactions. However, the stability of the protein also decreases due to thermal degradation. Holding the enzyme at a high enough temperature for a long period of time may cook the enzyme.

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Effect of Substrate Concentration

        Enzymes are not passive surfaces on which reactions take place but rather, are complex molecular machines that operate through a great diversity of chemical mechanisms.  According to Michaelis-Menten kinetics, enzyme-substrate reactions are actually comprised of two elementary reactions.  The first is the when the substrate forms a complex with the enzyme and then in the second, the complex decomposes to product and enzyme.                                                        _{k1                          k2}
                    Enzyme + Substrate  <----> Complex  ---->  Products + Enzyme
                                                      ^k-1
        According to this model, when the substrate concentration becomes high enough to entirely convert all of the enzyme to the complex form, the second step of the reaction becomes the rate-limiting step.  Therefore, the overall conversion to product becomes insensitive to further increases in substrate concentration.  The general expression for the rate of this reaction (velocity) becomes:
                                        v = d[P]/dt = k2*[complex] 


source :
http://www.rpi.edu/dept/chem-eng/Biotech-Environ/IMMOB/enzymeac.htm

The buffer

A buffer solution contains a conjugate acid – base pair with both the acid and base in reasonable concentrations. The acidic component reacts with added strong bases. The basic compenen reacts with added strong acids. A buffer solution is one which resists changes in pH when small quantities of an acid or an alkali are added to it. 

Acidic buffer solutions
An acidic buffer solution is simply one which has a pH less than 7. Acidic buffer solutions are commonly made from a weak acid and one of its salts - often a sodium salt.

Alkaline buffer solutions
An alkaline buffer solution has a pH greater than 7. Alkaline buffer solutions are commonly made from a weak base and one of its salts.
 

source from :
General Chemistry, whitten
http://www.chemguide.co.uk/physical/acidbaseeqia/buffers.html

The dogma centra of molecular biology

1) The concept of genes is historically defined on the basic of genetic inheritance of a phenotype. (Mendellian Inheritance)

2) The DNA an organism encodes the genetic information. It is made up of a double stranded helix composed of ribose sugars. 

Adenine(A), Citosine (C), Guanine (G) and Thymine (T).

[note that only 4 values nees be encode ACGT.. Which can be done using 2 bits.. But to allow redundant letter combinations (like N means any 4 nucleotides), one usually resorts to a 4 bit alphabet.]

3) Each side of the double helix faces it´s complementary base.

A-T, and G-C.

4) Biochemical process that read off the DNA always read it from the 5´´side towards the 3´ side. (replication and transcription).

5) A gene can be located on either the ´plus strand´ or the minus strand.  But rule 4) imposes the orientation of reading .. And rule 3 (complementarity) tells us to complement each base E.g.

If the sequence on the + strand is ACGTGATCGATGCTA, the – strand must be read off by reading the complement of this sequence going ´backwards´

e.g. TAGCATCGATCACGT

6) DNA information is copied over to mRNA that acts as a template to produce proteins.

 

 

We often concentrate on protein coding genes, because proteins are the building blocks of cells and the majority of bio-active molecules. (but let´s not forget the various RNA genes)

source from :
Hugues Sicotte NCBI Fundamentals in Sequence Analysis 1.(part 1) and http://crystal.uah.edu/~carter/protein/dogma.htm