Nucleic Acids

You will remember that we mentioned earlier that each protein is different because of its unique sequence of amino acids. But what controls how the amino acids arrange themselves to form the specific proteins that are needed by an organism? This task is for the gene. A gene contains DNA (deoxyribonucleic acid) which is a polymer that belongs to a class of compounds called the nucleic acids. DNA is the genetic material that organisms inherit from their parents. It is DNA that provides the genetic coding that is needed to form the specific proteins that an organism needs. Another nucleic acid is RNA (ribonucleic acid). The diagram in figure 2.14 shows an RNA molecule.

The DNA polymer is made up of monomers called nucleotides. Each nucleotide has three parts: a sugar, a phosphate and a nitrogenous base. DNA is a double-stranded helix (a helix is basically

nucleotide DNA polymer made up of four nucleotides

phosphate sugar nitrogenous base

Figure 2.14: Nucleotide monomers make up the RNA polymer a coil). Or you can think of it as two RNA molecules bonded together.

There are five different nitrogenous bases: adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U). It is the sequence of the nitrogenous bases in a DNA polymer that will determine the genetic code for that organism. Three consecutive nitrogenous bases provide the coding for one amino acid. So, for example, if the nitrogenous bases on three nucleotides are uracil, cytosine and uracil (in that order), one serine amino acid will become part of the polypeptide chain. The polypeptide chain is built up in this way until it is long enough (and with the right amino acid sequence) to be a protein. Since proteins control much of what happens in living organisms, it is easy to see how important nucleic acids are as the starting point of this process.

Interesting Fact

teresting

Fact

One example of this is a disease called sickle cell anaemia. Because of oneA single defect in even one nucleotide, can be devastating to an organism. wrong nucletide in the genetic code, the body produces a protein called sickle haemoglobin. Haemoglobin is the protein in red blood cells that helps to transport oxygen around the body. When sickle haemoglobin is produced, the red blood cells change shape. This process damages the red blood cell membrane, and can cause the cells to become stuck in blood vessels. This then means that the red blood cells, whcih are carrying oxygen, can’t get to the tissues where they are needed. This can cause serious organ damage. Individuals who have sickle cell anaemia generally have a lower life expectancy.

Table 2.2: Nitrogenouse base sequences and the corresponding amino acid Nitrogenous base sequence Amino acid

UUU Phenylalanine CUU Leucine UCU Serine UAU Tyrosine UGU Cysteine GUU Valine GCU Alanine GGU Glycine

Exercise: Nucleic acids

1. For each of the following, say whether the statement is true or false. If the statement is false, give a reason for your answer.

(a) Deoxyribonucleic acid (DNA) is an example of a polymer and a nucleotide is an example of a monomer.

(b) Thymine and uracil are examples of nucleotides.

(c) A person’s DNA will determine what proteins their body will produce, and therefore what characteristics they will have.

(d) An amino acid is a protein monomer.

(e) A polypeptide that consists of five amino acids, will also contain five nu- cleotides.

2. For each of the following sequences of nitrogenous bases, write down the amino acid/s that will be part of the polypeptide chain.

(a) UUU (b) UCUUUU

(c) GGUUAUGUUGGU

3. A polypeptide chain consists of three amino acids. The sequence of nitrogenous bases in the nucleotides of the DNA is GCUGGUGCU. Give the structural formula of the polypeptide.

2.7

Summary

• A polymer is a macromolecule that is made up of many repeating structural units called monomers which are joined by covalent bonds.

• Polymers that contain carbon atoms in the main chain are called organic polymers. • Organic polymers can be divided into natural organic polymers (e.g. natural rubber) or

synthetic organic polymers (e.g. polystyrene).

• The polymer polyethene for example, is made up of many ethene monomers that have been joined into a polymer chain.

• Polymers form through a process called polymerisation.

• Two examples of polymerisation reactions are addition and condensation reactions. • An addition reaction occurs when unsaturated monomers (e.g. alkenes) are added to

each other one by one. The breaking of a double bond between carbon atoms in the monomer, means that a bond can form with the next monomer. The polymer polyethene is formed through an addition reaction.

• In a condensation reaction, a molecule of water is released as a product of the reaction. The water molecule is made up of atoms that have been lost from each of the monomers. Polyesters and nylon are polymers that are produced through a condensation reaction. • The chemical properties of polymers (e.g. tensile strength and melting point) are deter-

mined by the types of atoms in the polymer, and by the strength of the bonds between adjacent polymer chains. The stronger the bonds, the greater the strength of the polymer, and the higher its melting point.

• One group of synthetic organic polymers, are the plastics.

• Polystyrene is a plastic that is made up of styrene monomers. Polystyrene is used a lot in packaging.

• Polyvinyl chloride (PVC) consists of vinyl chloride monomers. PVC is used to make pipes and flooring.

• Polyethene, or polyethylene, is made from ethene monomers. Polyethene is used to make film wrapping, plastic bags, electrical insulation and bottles.

• Polytetrafluoroethylene is used in non-stick frying pans and electrical insulation. • A thermoplastic can be heated and melted to a liquid. It freezes to a brittle, glassy state

when cooled very quickly. Examples of thermoplastics are polyethene and PVC.

• A thermoset plastic cannot be melted or re-shaped once formed. Examples of thermoset plastics are vulcanised rubber and melanine.

• It is not easy to recycle all plastics, and so they create environmental problems.

• Some of these environmental problems include issues of waste disposal, air pollution and recycling.

• A biological macromolecule is a polymer that occurs naturally in living organisms. • Examples of biological macromolecules include carbohydrates and proteins, both of which

are essential for life to survive.

• Carbohydrates include the sugars and their polymers, and are an important source of energy in living organisms.

• Glucose is a carbohydrate monomer. Glucose is the molecule that is needed for cellular respiration.

• The glucose monomer is also a building block for carbohydrate polymers such as starch, glycogen and cellulose.

• Proteins have a number of important functions. These include their roles in structures, transport, storage, hormonal proteins and enzymes.

• A protein consists of monomers called amino acids, which are joined by peptide bonds. • A protein has a primary, secondary and tertiary structure.

• An amino acid is an organic molecule, made up of a carboxyl and an amino group, as well as a carbon side chain of varying lengths.

• It is the sequence of amino acids that determines the nature of the protein.

• It is the DNA of an organism that determines the order in which amino acids combine to make a protein.

• DNA is a nucleic acid. DNA is a polymer, and is made up of monomers called nucleotides. • Each nucleotide consists of a sugar, a phosphate and a nitrogenous base. It is the sequence of the nitrogenous bases that provides the ’code’ for the arrangement of the amino acids in a protein.

Exercise: Summary exercise

1. Give one word for each of the following descriptions: (a) A chain of monomers joined by covalent bonds.

(b) A polymerisation reaction that produces a molecule of water for every two monomers that bond.

(c) The bond that forms between an alcohol and a carboxylic acid monomer during a polymerisation reaction.

(d) The name given to a protein monomer. (e) A six-carbon sugar monomer.

(f) The monomer of DNA, which determines the sequence of amino acids that will make up a protein.

2. For each of the following questions, choose the one correct answer from the list provided.

(a) A polymer is made up of monomers, each of which has the formula CH2=CHCN.

The formula of the polymer is: i. -(CH2=CHCN)n-

ii. -(CH2-CHCN)n-

iii. -(CH-CHCN)n-

iv. -(CH3-CHCN)n-

(b) A polymer has the formula -[CO(CH2)4CO-NH(CH2)6NH]n-. Which of

the following statements is true?

i. The polymer is the product of an addition reaction. ii. The polymer is a polyester.

iii. The polymer contains an amide linkage. iv. The polymer contains an ester linkage. (c) Glucose...

i. is a monomer that is produced during cellular respiration ii. is a sugar polymer

iii. is the monomer of starch

iv. is a polymer produced during photosynthesis

3. The following monomers are involved in a polymerisation reaction:

H2N C H H C O OH H2N C H H C O OH +

(a) Give the structural formula of the polymer that is produced. (b) Is the reaction an addition or condensation reaction?

(c) To what group of organic compounds do the two monomers belong? (d) What is the name of the monomers?

(e) What type of bond forms between the monomers in the final polymer? 4. The table below shows the melting point for three plastics. Suggest a reason

why the melting point of PVC is higher than the melting point for polyethene, but lower than that for polyester.

Plastic Melting point (0_C)

Polyethene 105 - 115

PVC 212

5. An amino acid has the formula H2NCH(CH2CH2SCH3)COOH.

(a) Give the structural formula of this amino acid.

(b) What is the chemical formula of the carbon side chain in this molecule? (c) Are there any peptide bonds in this molecule? Give a reason for your

Chapter 3

Reaction Rates - Grade 12

3.1

Introduction

Before we begin this section, it might be useful to think about some different types of reactions and how quickly or slowly they occur.

Exercise: Thinking about reaction rates Think about each of the following reactions: • rusting of metals

• photosynthesis

• weathering of rocks (e.g. limestone rocks being weathered by water) • combustion

1. For each of the reactions above, write a chemical equation for the reaction that takes place.

2. How fast is each of these reactions? Rank them in order from the fastest to the slowest.

3. How did you decide which reaction was the fastest and which was the slowest? 4. Try to think of some other examples of chemical reactions. How fast or slow

is each of these reactions, compared with those listed earlier?

In a chemical reaction, the substances that are undergoing the reaction are called the reactants, while the substances that form as a result of the reaction are called the products. The reaction rate describes how quickly or slowly the reaction takes place. So how do we know whether a reaction is slow or fast? One way of knowing is to look either at how quickly the reactants are used up during the reaction or at how quickly the product forms. For example, iron and sulfur react according to the following equation:

F e + S → F eS

In this reaction, we can observe the speed of the reaction by measuring how long it takes before there is no iron or sulfur left in the reaction vessel. In other words, the reactants have been used up. Alternatively, one could see how quickly the iron sulfide product forms. Since iron sulfide looks very different from either of its reactants, this is easy to do.

2M g(s) + O2→ 2MgO(s)

In this case, the reaction rate depends on the speed at which the reactants (solid magnesium and oxygen gas) are used up, or the speed at which the product (magnesium oxide) is formed.

Definition: Reaction rate

The rate of a reaction describes how quickly reactants are used up or how quickly products are formed during a chemical reaction. The units used are: moles per second (mols/second or mol.s−1_).

The average rate of a reaction is expressed as the number of moles of reactant used up, divided by the total reaction time, or as the number of moles of product formed, divided by the reaction time. Using the magnesium reaction shown earlier:

Average reaction rate of M g = moles M g used reaction time (s) or

Average reaction rate of O2=

moles O2 used

reaction time (s) or

Average reaction rate of M gO = moles M gO produced reaction time (s)

Worked Example 12: Reaction rates Question: The following reaction takes place:

4Li + O2→ 2Li2O

After two minutes , 4 g of Lithium has been used up. Calculate the rate of the reaction.

Answer

Step 1 : Calculate the number of moles of Lithium that are used up in the reaction.

n = m M =

4

6.94= 0.58mols

Step 2 : Calculate the time (in seconds) for the reaction. t = 2 × 60 = 120s

Step 3 : Calculate the rate of the reaction. Rate of reaction =

moles of Lithium used

time =

0.58

120 = 0.005 The rate of the reaction is 0.005 mol.s−1

Exercise: Reaction rates

1. A number of different reactions take place. The table below shows the number of moles of reactant that are used up in a particular time for each reaction.

Reaction Mols used up Time Reaction rate

1 2 30 secs

2 5 2 mins

3 1 1.5 mins

4 3.2 1.5 mins 5 5.9 30 secs

(a) Complete the table by calculating the rate of each reaction. (b) Which is the fastest reaction?

(c) Which is the slowest reaction?

2. Two reactions occur simultaneously in separate reaction vessels. The reactions are as follows:

M g + Cl2→ MgCl2

2N a + Cl2→ 2NaCl

After 1 minute, 2 g of MgCl2have been produced in the first reaction.

(a) How many moles of MgCl2 are produced after 1 minute?

(b) Calculate the rate of the reaction, using the amount of product that is produced.

(c) Assuming that the second reaction also proceeds at the same rate, calcu- late...

i. the number of moles of NaCl produced after 1 minute.

ii. the mass (in g) of sodium that is needed for this reaction to take place.

In document PhysicalScience_Gr12 (Page 66-75)