Biological Molecules - DNA and RNA

Question 1

What are nucleic acids?

Answer 1

Nucleic acids are a group of the most important molecules of which the best known are ribonucleic acid and deoxyribonucleic acid.

Question 2

What three components are individual nucleotides made up of?

Answer 2

• a pentose sugar (so called because it has five carbon atoms)
• a phosphate group
• a nitrogen-containing organic base (these are: cytosine, thymine, uracil, adenine and guanine)

Question 3

What is the nucleotide structure?

Answer 3

The pentose sugar, phosphate group and organic base are joined, as a result of condensation reactions, to form a single nucleotide (mononucleotide). Two mononucleotides may in turn be joined as a result of a condensation reaction between the deoxyribose sugar of one mononucleotide and the phosphate group of another. The bond formed between them is called a phosphodiester bond. The new structure is called a dinucleotide. The continued linking of mononucleotides in this way forms a long chain known as a polynucleotide.

Question 4

What is the structure of ribonucleic acid (RNA)?

Answer 4

Ribonucleic acid is a polymer made up of nucleotides. It is a single, relatively short, polynucleotide chain in which the pentose sugar is always ribose and the organic bases are adenine, guanine, cytosine and uracil. One type of RNA transfers genetic information from DNA to the ribosomes. The ribosomes themselves are made up of proteins and another type of RNA. A third type of RNA is involved in protein synthesis.

Question 5

What is the structure of deoxyribose nucleic acid (DNA)?

Answer 5

In DNA the pentose sugar is deoxyribose and the organic bases are adenine, thymine, guanine and cytosine. DNA is made up of two strands of nucleotides (polynucleotides). Each of the two strands is extremely long, and they are joined together by hydrogen bonds formed between certain bases. In its simplified form, DNA can be thought of as a ladder in which the phosphate and deoxyribose molecules alternate to form the uprights and the organic bases pair together to form the rungs.

Question 6

What is base pairing?

Answer 6

The bases on the two strands of DNA attach to each other by hydrogen bonds. It is these hydrogen bonds that hold the two strands together. The base pairing is specific:

• adenine always pairs with thymine (2 hydrogen bonds)
• guanine always pairs with cytosine (3 hydrogen bonds)

As a result of these pairings, adenine is said to be complementary to thymine and guanine is said to be complementary to cytosine.

It follows that the quantities of adenine and thymine in DNA are always the same, and so are the quantities of guanine and cytosine. However, the ratio of adenine and thymine to guanine and cytosine varies from species to species.

Question 7

What is the double helix?

Answer 7

In order to appreciate the structure of DNA, you need to imagine the ladder-like arrangement of the two polynucleotide chains being twisted. In this way, the uprights of phosphate and deoxyribose wind around one another to form a double helix. They form the structural backbone of the DNA molecule.

Question 8

Why is DNA a stable molecule?

Answer 8

DNA is a stable molecule because:

• The phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.
• Hydrogen bonds link the organic base pairs forming bridges (rungs) between the phosphodiester uprights. As there are more hydrogen bonds between cytosine and guanine, the higher the proportion of C-G pairings, the more stable the DNA molecule.

There are other interactive forces between the base pairs that hold the molecule together (= base stacking).

Question 9

What is the difference between each molecule of DNA?

Answer 9

In every molecule of DNA, the phosphate group, the deoxyribose and the four bases are always the same. What differs between one DNA molecule and another are the proportions, and more importantly the sequence, of each of the four bases.

Question 10

What is the function of DNA?

Answer 10

DNA is the hereditary material responsible for passing genetic information from cell to cell and generation to generation. There is an almost infinite variety of sequences of bases along the length of a DNA molecule. It is this variety that provides the genetic diversity within living organisms.

Question 11

How is the DNA molecule adapted to carry out its function?

Answer 11

• It is a very stable structure which normally passes from generation to generation without significant change. Most mutations are repaired, so persistent mutations are rare.
• Its two separate strands are joined only with hydrogen bonds, which allow them to separate during DNA replication and protein synthesis.
• It is an extremely large molecule and therefore carries an immense amount of genetic information.
• By having the base pairs within the helical cylinder of the deoxyribose-phosphate backbone, the genetic information is to some extent protected from being corrupted by outside chemical and physical forces, as the nitrogen containing organic bases are more chemically reactive.
• Base pairing leads to DNA being able to replicate and to transfer information as mRNA.

Question 12

What does the function of DNA depend on?

Answer 12

The function of DNA depends on the sequence of base pairs that it possesses.

Question 13

What is the timeline of the discovery of DNA?

Answer 13

• 1856: Mendel’s inheritable factors.
• 1869: Miescher discovers ‘nuclein’.
• 1911: Morgan shows chromosomes contain genes.
• 1928: Griffith mixes strains of bacteria.
• 1929: Levene finds deoxyribose and bases.
• 1944: Avery identifies DNA as a transforming agent.
• 1950: Chargraff discovers ratio between bases.
• 1952: Franklin’s x-ray crystallography of DNA.
• 1952: Hershey and Chase show DNA is inheritable in viruses.
• 1953: Watson and Crick propose double helix structure of DNA.

Question 14

What are two rings called? What is one ring called?

Answer 14

two rings = “purine”

one ring = “pyrimidine”

Question 15

How do the two nucleotide strands run?

Answer 15

anti-parallel

Question 16

What is chromatin?

Answer 16

The DNA double helix is wrapped around histone proteins. This is called a chromatin.

Question 17

What is a chromosome?

Answer 17

one strand of DNA

Question 18

What is a gene?

Answer 18

a section of DNA on a chromosome (one gene codes for one polypeptide)

Question 19

What is a locus?

Answer 19

the position of a gene on a chromosome

Question 20

What are alleles?

Answer 20

different forms of the same gene

Question 21

What pairs do chromosomes occur in?

Answer 21

in homologous pairs; they contain the same genes at the same loci

Question 22

What DNA doesn’t code for proteins?

Answer 22

1. DNA between genes

2. Introns within genes

Question 23

What are exons?

Answer 23

sections of a gene that code for the polypeptide

Question 24

What is DNA helicase?

Answer 24

An enzyme that breaks the hydrogen bonds between the two DNA strands in the DNA molecule that is going to be replicated.

Question 25

What is DNA polymerase?

Answer 25

An enzyme that catalyses the condensation reactions between the new nucleotides in the synthesis of the new DNA strand. It joins the DNA nucleotides, forming phosphodiester bonds.

Question 26

What is a phosphodiester bond?

Answer 26

The bond formed by a condensation reaction between the phosphate group of one nucleotide and the pentose sugar of another nucleotide.

Question 27

What is semiconservative replication?

Answer 27

The process in which the double helix of a DNA molecule unwinds and each strand acts as a template on which a new strand is constructed.

Question 28

What was Griffith’s Streptococcus experiment?

Answer 28

R strain: mouse lives -> R strain is benign

S strain: mouse dies -> S strain is virulent

Heat-killed S strain: mouse lives -> killed S strain cells are benign

R strain + heat-killed S strain: mouse dies -> live R strain cells were transformed to S strain

Question 29

How are all cells derived?

Answer 29

Except for zygotes that are formed by cellular fusion, all of the cells that make up multicellular organisms are derived from existing cells by the process of division.

Question 30

What are the two main stages that cell division occurs in?

Answer 30

• Nuclear division: is the process by which the nucleus divides. There are two types of nuclear division, mitosis and meiosis.
• Cytokinesis: follows nuclear division and is the process by which the whole cell divides.

Question 31

What happens before a nucleus divides?

Answer 31

Before a nucleus divides its DNA must be replicated (copies). This is to ensure that all the daughter cells have the genetic information to produce the enzymes and other proteins that they need.

The process of DNA replication is very precise because all the new cells are more or less genetically identical to the original one.

Question 32

What are the requirements for semi-conservative replication to take place?

Answer 32

• The four types of nucleotides, each with their bases of adenine, guanine, cytosine or thymine, must be present.
• Both strands of the DNA molecule act as a template for the attachment of these nucleotides.
• The enzyme DNA polymerase.
• A source of chemical energy is required to drive the process.

Question 33

What is the process of semi-conservative replication?

Answer 33

1. A representative portion of DNA, which is about to undergo replication. The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.
2. The enzyme DNA helicase causes the two strands of the DNA to separate by breaking the hydrogen bonds that join the complementary bases together.
3. As a result, the double helix separates into its two strands and unwinds.
4. Each exposed polynucleotide strand then acts as a template to which complementary free nucleotides that have been activated bind by specific base pairing.
5. Once the activated nucleotides are bound, they are joined together by DNA polymerase which makes phosphodiester bonds by condensation reactions to form the ‘missing’ polynucleotide strand on each of the two original polynucleotide strands of DNA. The remaining unpaired bases continue to attract their complementary nucleotides.
6. Finally, all the nucleotides are joined to form a complete polynucleotide chain using DNA polymerase. In this way, two identical strands of DNA are formed. As each strand retains half of the original DNA material, this method of replication is called the semi-conservative method.

Question 34

What is the conservative model?

Answer 34

The conservative model suggested that the original DNA molecule remained intact and that a separate daughter DNA copy was built up from the new molecules of deoxyribose, phosphate and organic bases. Of the two molecules produced, one would be made of entirely new material while the other would be entirely original material.

Question 35

What is the semi-conservative model?

Answer 35

The semi-conservative model proposed that the original DNA molecule split into two separate strands, each of which then replicated its mirror (i.e. the missing half). Each of the two new molecules would therefore have one strand of new material and one strand of original material.

Question 36

What did Meselsohn and Stahl base their work on?

Answer 36

• all the bases in DNA contain nitrogen
• nitrogen has two forms: the lighter 14N and the isotope 15N, which is heavier
• bacteria will incorporate nitrogen from their growing medium into any new DNA that they make

Question 37

Summarise Meselsohn and Stahl’s experiments to determine the nature of DNA replication.

Answer 37

1. E.coli bacteria grown in 14N medium -> DNA extracted from bacteria -> DNA extract suspended in special solution -> DNA suspension centrifuged -> control: both strands light (14N)
2. Bacteria grown in 15N medium for many generations -> DNA extracted from bacteria -> DNA extract suspended in special solution -> DNA suspension centrifuged -> parents (generation zero): both strands are heavy (15N)
3. Bacteria transferred to 14N medium and samples removed at intervals -> after one generation, after two generations, after three generations -> DNA extracted from bacteria -> DNA extract suspended in special solution -> DNA suspension centrifuged -> first generation: one heavy (15N) and one light (14N) strand giving a mixed/intermediate DNA molecule, second generation: one light and one mixed/intermediate DNA molecule, third generation: mostly light

Question 38

Griffith found that living bacteria of the harmful form were isolated from the mice with pneumonia. What are the explanations for this?

Answer 38

• Experimental error, for example, the harmful forms in the mixture were not all killed.
• The living safe form had mutated into the harmful form. This is possible but extremely unlikely, especially given that the experiment was repeated many times with the same result.
• Pneumonia is caused by a toxin. The harmful form of the bacterium has the information on how to make the toxin but, being dead, cannot do so. The safe form has the means of making the toxin but lacks the information on how to do so. The information on how to make the toxin may have been transferred from the harmful form to the safe form, which then produced it.

Question 39

What series of experiments were carried out to investigate the third explanation?

Answer 39

• The living harmful bacteria that were found in the mice with pneumonia, were collected.
• Various substances were isolated from these bacteria and purified.
• Each substance was added to suspensions of living safe bacteria to see whether it would transform them into the harmful form.
• The only substance that produced this transformation was purified DNA.
• When an enzyme that breaks down DNA was added, the ability to carry out the transformation ceased.

Question 40

Does viral protein or viral DNA possess the instructions that the bacteria use to make new viruses?

Answer 40

• It had been observed that viruses infect bacteria, causing the bacteria to make more viruses.
• As the virus is made up of just protein and DNA, one or the other must possess the instructions that the bacteria use to make new viruses.
• The protein and DNA in the viruses were each labelled with a different radioactive element.
• One sample of bacteria was infected by viruses with radioactive protein while another sample was infected by viruses with radioactive DNA.
• In a later stage, the viruses and bacteria in both samples were separated from one another.
• Only the sample with bacteria that had been infected by viruses labelled with radioactive DNA showed signs of radioactivity.

Question 41

What is prime location?

Answer 41

In order to understand how nucleotides are arranged in nucleic acids, it is necessary to know how the carbon atoms in the pentose molecule are numbered. Of particularly importance is the numbering of the 3’ (3-prime) and 5’ (5-prime) carbon atoms. The 5’ carbon has an attached phosphate group, while the 3’ has a hydroxyl group.

When nucleotides are organised into the double strands of a DNA molecule, one strand runs in the 5’ and 3’ direction while the other runs the opposite way - in the 3’ and 5’ direction. The two strands are therefore said to be antiparallel.

Nucleic acids can only be synthesised ‘in viro’ in the 5’-to-3’ direction. This is because the enzyme DNA polymerase that assembles nucleotides into a DNA molecule can only attach nucleotides to the hydroxyl (OH) group on the 3’ carbon molecule.

Question 42

How are the two DNA strands separated?

Answer 42

The DNA form bubbles along the strands (origin of replication). Over time the bubbles get larger until they completely pull apart.

Question 43

What is the difference between the conservative model, the semi-conservative model, and the dispersive model?

Answer 43

Conservative model: The parental double helix remains intact an an all-new copy is made.

Semi-conservative model: The two strands of the parental molecule separate, and each functions as a template for synthesis of a new complementary strand.

Dispersive model: Each strand of both daughter molecules contains a mixture of old and newly synthesized parts.

Question 44

Why is it important to have the bases on the inside of the double helix?

Answer 44

because it protects them from reactions with free radicals

Question 45

What is the meaning of antiparallel strands in the DNA molecule?

Answer 45

The phosphate groups at the start of the DNA strands are in opposite positions.

When nucleotides are organised into the double strands of a DNA molecule, one strand runs in the 5’ and 3’ direction while the other runs the opposite way - in the 3’ and 5’ direction. The two strands are therefore said to be antiparallel.

Question 46

What is the difference between the leading strand and the lagging strand?

Answer 46

Nucleotides are assembled in a continuous fashion in the leading strand whereas fragments are created in the lagging strand.

Question 47

What is an Okazaki fragment?

Answer 47

The fragments created in the lagging strand, which are later joined to form one continuous length by DNA ligase.

Question 48

What is a replication fork?

Answer 48

The region where the nucleotides are added. The position of the replication fork moves along the chromosome as replication progresses.

Question 49

Why does DNA polymerase only work in one direction?

Answer 49

Nucleic acids can only be synthesised ‘in viro’ in the 5’-to-3’ direction. This is because the enzyme DNA polymerase that assembles nucleotides into a DNA molecule can only attach nucleotides to the hydroxyl (OH) group on the 3’ carbon molecule.

Question 50

What is the purpose of DNA replication?

Answer 50

DNA replication is a necessary preliminary step for cell division (both mitosis and meiosis). This process ensures that each resulting cell receives a complete set of genes from the original cell. After DNA replication, each chromosome is made up of two chromatids, joined at the centromere. Each chromatid contains half original (parent) DNA and half new (daughter) DNA. The two chromatids will become separated during cell division to form two separate chromosomes.

Question 51

What happens in stage one of DNA replication, when the DNA molecule is unwinding?

Answer 51

A normal chromosome consists of an unreplicated DNA molecule. Prior to cell division, this long molecule of double stranded DNA must be replicated. It is untwisted at high speed at its replication fork by two enzymes: helicase unwinds the parental strands and DNA gyrase then relieves the strain that this generates by cutting, winding and rejoining the DNA strands.

Question 52

What happens in stage two of DNA replication, when the new DNA strands are made?

Answer 52

The formation of new DNA is carried out mostly by an enzyme complex called DNA polymerase, and a series of proteins that causes the two strands to break apart. Nucleotides can only be added in the 5’ to 3’ direction. This means that on one side (the leading strand), nucleotides are assembled in a continuous fashion, while on the other side (the lagging strand) fragments (called Okazaki fragments) are created. These fragments, between 1000-2000 nucleotides long, are later joined to form one continuous length.

Question 53

How are the new strands of DNA constructed from free nucleotides?

Answer 53

using the parent strand as a template

Question 54

What happens in stage three of DNA replication, when the DNA molecule is rewinded?

Answer 54

Each of the two new double-helix DNA molecules has one strand of the original DNA and one strand that is newly synthesised. The two DNA molecules rewind into their double-helix shape again. Each double-helix is then coiled around histone proteins and further wrapped up to form separate chromatids (still joined by a common centromere). The replicated chromosome has twice the DNA as a regular chromosome. The two chromatids will become separated in the cell division process to form two separate chromosomes.

Question 55

When does DNA replication occur?

Answer 55

DNA replication occurs during interphase of the cell cycle at an astounding rate.

Question 56

What does DNA helicase do?

Answer 56

Splits and unwinds the double stranded DNA molecule.

Question 57

What does DNA gyrase (topoisomerase) do?

Answer 57

Relieves the torsional strain that unwinding the parent strands generates by cutting, winding and rejoining the DNA strands.

Question 58

What does RNA polymerase/primase do?

Answer 58

Synthesises a short RNA primer which is later removed.

Question 59

What does DNA polymerase III do?

Answer 59

Extends RNA primer with short lengths of complementary DNA from 5’ to 3’.

Question 60

What does DNA polymerase I do?

Answer 60

Digests RNA primer and replaces it with DNA.

Question 61

What DNA ligase do?

Answer 61

Joins neighbouring fragments together.

Question 62

How are the enzymes found?

Answer 62

Many of the enzymes are found clustered together as enzyme complexes. These enzymes are also able to ‘proof-read’ the new DNA strand as it is made and correct mistakes. The polymerase enzyme can only work in one direction, so that one new strand is constructed as a continuous length (the leading strand) while the other new strand is made in short segments to be later joined together (the lagging strand).

Question 63

How are nucleotides present?

Answer 63

The nucleotides are present as deoxynucleoside triphosphates. When hydrolysed, these provide the energy for incorporating the nucleotide into the strand.

Question 64

What is DNA and RNA?

Answer 64

DNA and RNA are important information-carrying molecules. In all living cells, DNA holds genetic information and RNA transfers genetic information from DNA to the ribosomes.