chapter 3 p5

Question 1

Nucleic acids are

Answer 1

large molecules that were discovered in cell nuclei - hence their name.
There are two types of nucleic acid - DNA and RNA, and both have roles in the storage and transfer of genetic information and the synthesis of polypeptides (proteins).
They are the basis for heredity.

Question 2

Nucleic acids contain the elements

Answer 2

carbon, hydrogen, oxygen, nitrogen and phosphorus.
They are large polymers formed from many nucleotides (the monomers) linked together in a chain.

Question 3

An individual nucleotide is made up of three components:

Answer 3

• a pentose monosaccharide (sugar), containing five carbon atoms
• a phosphate group, -PO,, an inorganic molecule that is acidic and negatively charged
• a nitrogenous base - a complex organic molecule containing one or two carbon rings in its structure as well as nitrogen.

Question 4

Nucleotides are linked together

Answer 4

• by condensation reactions to form a polymer called a polynucleotide.
• The phosphate group at the fifth carbon of the pentose sugar (5’) of one nucleotide forms a covalent bond with the hydroxyl (OH) group at the third carbon (3’) of the pentose sugar of an adjacent nucleotide.
• These bonds are called phosphodiester bonds.
• This forms a long, strong sugar-phosphate ‘backbone’ with a base attached to each sugar
• The phosphodiester bonds are broken by hydrolysis, the reverse of condensation, releasing the individual nucleotides.

Question 5

Deoxyribonucleic acid (DNA):

Answer 5

the sugar in deoxyribonucleic acid (DNA) is deoxyribose - a sugar with one fewer oxygen atoms than ribose, as shown in Figure 3.

The nucleotides in DNA each have one of four different bases.
This means there are four different DNA nucleotides The four bases can be divided into two groups:

Question 6

The four bases can be divided into two groups:

Answer 6

• Pyrimidines - the smaller bases, which contain single carbon ring structures - thymine (T) and cytosine (C)
• Purines - the larger bases, which contain double carbon ring structures - adenine (A) and guanine (G).

Question 7

Answer 7

Question 8

The double helix:

Answer 8

• The DNA molecule varies in length from a few nucleotides to millions of nucleotides.
• It is made up of two strands of polynucleotides coiled into a helix, known as the DNA double helix
• The two strands of the double helix are held together by hydrogen bonds between the bases, much like the rungs of a ladder.
• Each strand has a phosphate group (5’) at one end and a hydroxy! group (3’) at the other end.
• The two parallel strands are arranged so that they run in opposite directions - they are said to be antiparallel.
• The pairing between the bases allows DNA to be copied and transcribed - key properties required of the molecule of heredity.

Question 9

Answer 9

Question 10

Answer 10

Question 11

Base pairing rules:
p1

Answer 11

• Adenine and thymine are both able to form two hydrogen bonds and always join with each other.
• Cytosine and guanine form three hydrogen bonds and so also only bind to each other.
• This is known as complementary base pairing.
• These rules mean that a small pyrimidine base always binds to a larger purine base.

Question 12

Base pairing rules:
p2

Answer 12

• This arrangement maintains a constant distance between the DNA ‘backbones’, resulting in parallel polynucleotide chains.
• Complementary base pairing means that DNA always has equal amounts of adenine and thymine and equal amounts of cytosine and guanine.
• This was known long before the detailed structure of DNA was determined by Watson and Crick in 1953.
• It is the sequence of bases along a DNA strand that carries the genetic information of an organism in the form of a code.

Question 13

Answer 13

Question 14

Ribonucleic acid (RNA): p1

Answer 14

Ribonucleic acid (RNA) plays an essential role in the transfer of genetic information from DNA to the proteins that make up the enzymes and tissues of the body.
DNA stores all of the genetic information needed by an organism, which is passed on from generation to generation.
However, the DNA of each eukaryotic chromosome is a very long molecule, comprising many hundreds of genes, and is unable to leave the nucleus in order to supply the information directly to the sites of protein synthesis.

Question 15

Ribonucleic acid (RNA): p2

Answer 15

To get around this problem, the relatively short section of the long DNA molecule corresponding to a single gene is transcribed into a similarly short messenger RNA (mRNA) molecule.
Each individual mRNA is therefore much shorter than the whole chromosome of DNA.
It is a polymer composed of many nucleotide monomers.
RNA nucleotides are different to DNA nucleotides as the pentose sugar is ribose rather than deoxyribose (Figure 3) and the thymine base is replaced with the base uracil (U) (see Figure 9).

Question 16

Ribonucleic acid (RNA): p3

Answer 16

Like thymine, uracil is a pyrimidine that forms two hydrogen bonds with adenine.
Therefore the base pairing rules still apply when RNA nucleotides bind to DNA to make copies of particular sections of DNA.
The RNA nucleotides form polymers in the same way as DNA nucleotides - by the formation of phosphodiester bonds in condensation reactions.
The RNA polymers formed are small enough to leave the nucleus and travel to the ribosomes, where they are central in the process of protein synthesis.
After protein synthesis the RNA molecules are degraded in the cytoplasm.
The phosphodiester bonds are hydrolysed and the RNA nucleotides are released and reused.

Question 17

Answer 17

Question 18

DNA extraction:
DNA can be extracted from plant material using the following procedure: p1

Answer 18

Grind sample in a mortar and pestle - this breaks down the cell walls.
Mix sample with detergent - this breaks down the cell membrane, releasing the cell contents into solution As it disrupts membrane structure; phospholipids form suspension in aqueous solution
Add salt - this breaks the hydrogen bonds between the DNA and water molecules.
Add protease enzyme - this will break down the proteins associated with the DNA in the nuclei.

Question 19

DNA extraction:
DNA can be extracted from plant material using the following procedure: p2

Answer 19

Add a layer of alcohol (ethanol) on top of the sample - alcohol causes the DNA to precipitate out of solution.
The DNA will be seen as white strands forming between the layer of sample and layer of alcohol (Figure 9). The DNA can be picked up by spooling it onto a glass rod.
The temperature needs to be kept low throughout this procedure to reduce activity of enzymes (1); reduce breakdown of DNA (1)

Question 20

DNA replication process

Answer 20

Cells divide to produce more cells needed for growth or repair of tissues.
The two daughter cells produced as a result of cell division are genetically identical to the parent cell and to each other. In other words, they contain DNA with a base sequence identical to the original parent cell.
When a cell prepares to divide, the two strands of DNA double helix separate and each strand serves as a template for the creation of a new double-stranded DNA molecule.
The complementary base pairing rules ensure that the two new strands are identical to the original.
This process is called DNA replication.

Question 21

Semi-conservative replication:
p1

Answer 21

For DNA to replicate, the double helix structure has to unwind and then separate into two strands, so the hydrogen bonds holding the complementary bases together must be broken (Figure 1c).
Free DNA nucleotides will then pair with their complementary bases, which have been exposed as the strands separate.
Hydrogen bonds are formed between them.

Question 22

Semi-conservative replication:
p2

Answer 22

Finally, the new nucleotides join to their adjacent nucleotides with phosphodiester bonds (Figure 1d).
In this way, two new molecules of DNA are produced. Each one consists of one old strand of DNA and one new strand.
This is known as semi-conservative (meaning half the same) replication.

Question 23

Roles of enzymes in replication: p1

Answer 23

DNA replication is controlled by enzymes, a class of proteins that act as catalysts for biochemical reactions.
Enzymes are only able to carry out their function by recognising and attaching to specific molecules or particular parts of the molecules.
Before replication can occur, the unwinding and separating of the two strands of the DNA double helix is carried out by the enzyme DNA helicase.

Question 24

Roles of enzymes in replication: p2

Answer 24

It travels along the DNA backbone, catalysing reactions that break the hydrogen bonds between complementary base pairs as it reaches them.
This can be thought of as the strand ‘unzipping’.
Free nucleotides pair with the newly exposed bases on the template strands during the ‘unzipping’ process.
A second enzyme, DNA polymerase catalyses the formation of phosphodiester bonds between these nucleotides.

Question 25

Continuous and discontinuous replication: p1

Answer 25

DNA polymerase always moves along the template strand in the same direction It can only bind to the 3' (OH) end, so travels in the direction of 3' to 5'. As DNA only unwinds and unzips in one direction, DNA polymerase has to replicate each of the template strands in opposite directions. The strand that is unzipped from the 3' end can be continuously replicated as the strands unzip. This strand is called the leading strand and is said to undergo continuous replication.

Question 26

Continuous and discontinuous replication: p2

Answer 26

The other strand is unzipped from the 5' end, so DNA polymerase has to wait until a section of the strand has unzipped and then work back along the strand. This results in DNA being produced in sections (called Okazaki fragments), which then have to be joined. This strand is called the lagging strand and is said to undergo discontinuous replication.

Question 27

Describe the difference between continuous and discontinuous replication:

Answer 27

Continuous replication – DNA polymerase binds to the end of a strand, free DNA nucleotides added without any breaks; discontinuous replication – DNA polymerase cannot bind to the end of a strand, free DNA nucleotides added in sections, sections then joined.

Question 28

Using your knowledge of enzymes, explain why DNA polymerase does not catalyse the joining of Okazaki fragments into a single strand but a different enzyme (DNA ligase) is used.

Answer 28

Enzymes are (substrate) specific (1); DNA polymerase catalyses the joining of nucleotides (1); nucleotides have a different shape to Okazaki fragments (1).

Question 29

Answer 29

Question 30

Replication errors:

Answer 30

Sequences of bases are not always matched exactly, and an incorrect sequence may occur in the newly-copied strand. These errors occur randomly and spontaneously and lead to a change in the sequence of bases, known as a mutation.

Question 31

Genetic code:

Answer 31

DNA must carry the instructions' or 'blueprint' needed to synthesise the many different proteins needed by these organisms. Proteins are the foundation for the different physical and biochemical characteristics of living things. They are made up of a sequence of amino acids, folded into complex structures. Therefore DNA must code for a sequence of amino acids. This is called the genetic code.

Question 32

A triplet code:

Answer 32

The instructions that DNA carries are contained in the sequence of bases along the chain of nucleotides that make up the two strands of DNA. The code in the base sequences is a simple triplet code. It is a sequence of three bases, called a codon. Each codon codes for an amino acid. A section of DNA that contains the complete sequence of bases (codons) to code for an entire protein is called a gene. The genetic code is universal - all organisms use this same code, although the sequences of bases coding for each individual protein will be different.

Question 33

Degenerate code: p1

Answer 33

there are four different bases, which means there are 64 different base triplets or codons possible (43 or 4 x 4 x 4). This includes one codon that acts as the start codon when it comes at the beginning of a gene, signalling the start of a sequence that codes for a protein. If it is in the middle of a gene, it codes for the amino acid methionine. There are also three 'stop' codons that do not code for any amino acids and signal the end of the sequence.

Question 34

Degenerate code: p2

Answer 34

Having a single codon to signal the start of a sequence ensures that the triplets of bases (codons) are read 'in frame'. In other words the DNA base sequence is 'read' from base 1, rather than base 2 or 3. So the genetic code is non-overlapping. As there are only 20 different amino acids that regularly occur in biological proteins, there are a lot more codons than amino acids. Therefore, many amino acids can be coded for by more than one codon, see Figure 4. Due to this, the code is known as degenerate.

Question 35

a codon

Answer 35

Question 36

Answer 36