Nucleotides and Nucleic Acids

Question 1

What are the types of nucleic acid?

Answer 1

There are two types of nucleic acid: deoxyribosnucleic acid (DNA) and ribonucleic acid (RNA).

Question 2

What is the role of nucleic acid?

Answer 2

The role of a nucleic acid is to provide the information to build an organism. The structures of nucleotides and nucleic acids allows an understanding of their roles in the storage and use of genetic information and cell metabolism.

Question 3

What are the monomers of nucleic acids?

Answer 3

The monomers of nucleic acids are nucleotides, which join to make polynucleotides (nucleic acids) – the polymer

Question 4

Describe the role of a nucleotide.

Answer 4

1. Form the monomers of nucleic acids
2. Become phosphorylated nucleotides when they contain more than one phosphate group – i.e. ADP or ATP
3. Help regulate metabolic pathways
4. May be components of coenzymes – i.e. NADP is used in photosynthesis

Question 5

Describe the structure of a single nucleotide.

Answer 5

One phosphate, one pentose (five carbon) sugar, a nitrogenous base

Question 6

Describe the structure of phosphorylated nucleotide.

Answer 6

• 1 phosphate group – AMP (adenosine monophosphate)
• 2 phosphate groups – ADP (adenosine diphosphate)
• 3 phosphate groups – ATP (adenosine triphosphate)

Question 7

Where is deoxyribonucleic acid found?

Answer 7

In the nuclei of all eukaryotic cells. In the cytoplasm of prokaryotic cells and some viruses.

Question 8

What is the role of deoxyribonucleic acid?

Answer 8

It carries coded instructions used in the development and functioning of all known living organisms. Codes for proteins. It is hereditary material.

Question 9

What is the structure of deoxyribonucleic acid?

Answer 9

A molecule of DNA consists of two polynucleotide strands – held by a sugar-phosphate backbone. DNA molecules are very long – can carry a lot of coded information. DNA is a long-chain polymer made up of many repeating nucleotide units to make a polynucleotide. Each nucleotide in a DNA molecule contains a phosphate group, deoxyribose sugar, an organic nitrogenous base (A/T/C/G).

Question 10

List the nitrogenous bases.

Answer 10

A – adenine
T – thymine
C – cytosine
G – guanine
U – uracil

There are four different nucleotides in DNA (A/T/C/G) and in RNA (A/U/C/G) and it is only the bases that differs between each nucleotide.

Question 11

Describe the two types of bases.

Answer 11

There are two types of bases - purine and pyrimidine bases. A purine will always and only pair up with a pyrimidine – complementary base pairing. The bases pair: in DNA: A-T (2 hydrogen bonds) and C-G (3 hydrogen bonds), in RNA: A-U and C-G.

Question 12

Describe purine bases.

Answer 12

They have two rings in their structure. Purine bases are adenine (A) and guanine (G).

Remember: Pure As Gold (Purine Adenine Guanine).

Question 13

Describe pyrimidine bases.

Answer 13

They have one ring in their structure. Smaller than a purine base.

Remember: CUT (cytosine uracil thymine).

Question 14

Describe how to form a polynucleotide of DNA.

Answer 14

A condensation reaction between the phosphate group of one nucleotide and the sugar of another nucleotide joins the two together, forming a phosphodiester bond. As nucleotides are bonded together, the ‘backbone’ of the molecule forms consisting of a repeating sugar phosphate chain. The organic nitrogenous bases project inwards from the backbone. DNA forms when two polynucleotide strands come together. They form a ‘ladder’ – the sugar-phosphate backbone forms the uprights and the bases form the rungs. The two DNA strands run parallel to each other because the space between them is taken up by nitrogenous bases projecting inwards. The strands run in opposite directions – they are anti-parallel. In a complete DNA molecule, the antiparallel chains twist to form the final structure – the double helix.

Question 15

Describe the importance of hydrogen bonding between DNA strands.

Answer 15

The bases of one chain link up the bases of the other by hydrogen bonding. This is important because it holds the strands together, leads to coiling of the molecule – very stable structure with bases protected in the middle and easily broken to allow molecules to unzip for transcription and DNA replication. The base pairs A-T – have 2 hydrogen bonds and C-G – have 3 hydrogen bonds, making the rungs on the DNA ladder the same width.

Question 16

Describe complementary base pairing.

Answer 16

The chains are always the same distance apart because the bases pair up in a specific way – pyrimidine on one side and purine on the other. A-T and C-G pair up in DNA / A-U and C-G in RNA – this is complementary base pairing. The base pairs A-T – have 2 hydrogen bonds and C-G – have 3 hydrogen bonds, making the rungs on the DNA ladder the same width.

Question 17

How is nucleotide mismatch prevented between the two strands?

Answer 17

Number of hydrogen bond attraction points. Size of the base: C won’t match with C as the bases will be too far to form hydrogen bonds, G won’t match with A because they are too long to fit side by side, T won’t match with G as there would be a mismatch in the number and orientation of the hydrogen bonds.

Question 18

How is DNA found in eukaryotes?

Answer 18

Majority of the DNA is in the nucleus. Each large DNA molecule is wound around histone proteins into chromosomes. Loops of DNA (no histones) are found in the mitochondria and chloroplasts.

Question 19

How is DNA found in prokaryotes?

Answer 19

DNA is in a loop within the cytoplasm. It is not wound around histones and is naked. Some have plasmids (circles of DNA).

Question 20

Describe the structure of RNA.

Answer 20

A phosphate group, ribose sugar, nitrogenous base (A-U and G-C). Single stranded. Nucleotides are joined by phosphodiester bonds – via condensation reactions.

Question 21

Describe the role of RNA.

Answer 21

Involved with using information from DNA to make proteins – protein synthesis. Molecules of RNA can be made to be complementary to molecules of DNA as exposed DNA nucleotides can have free RNA nucleotides hydrogen bonded to them, as their bases pair the same way – the sugar-phosphate backbone seals up to form a chain of RNA nucleotides.

Question 22

Describe the process of DNA replication.

Answer 22

1. In preparation for cell division, DNA replication takes place
2. The DNA double helix uncoils – catalysed by a GYRASE enzyme
3. DNA ‘unzips’ – the hydrogen bonds are broken – catalysed by the enzymes DNA HELICASE
4. This means the hydrogen bonds between complementary base pairs break
5. Free phosphorylated nucleotides are present in the nucleus
6. Free nucleotides form hydrogen bonds with exposed nucleotides according to base pairing rules – C-G (3 hydrogen bonds) and A-T (2 hydrogen bonds)
7. Free nucleotides are added to the 3’ end on the growing strand – catalysed by the enzyme DNA POLYMERASE
8. One strand is formed continuously – this is the leading strand
9. The other strand is formed in sections due to the antiparallel nature of the DNA double helix – this is the lagging strand
10. The Okazaki fragments formed during the formation of the lagging strand are joined by covalent bonds, sealing the backbone
11. Covalent bonds form between the phosphate of one nucleotide and the sugar of the next, forming the backbone – catalysed by the enzyme DNA LIGASE (only involved in the lagging strand)
12. The process continues all the way along the molecule until two new DNA molecules are formed – each is an exact copy of the original due to base-pairing rules.
13. This is SEMI-CONSERVATIVE REPLICATION because each DNA molecule consists of one conserved strand and one newly-built strand.

Question 23

When is DNA replication required?

Answer 23

1. When a cell divides, each new cell must receive a full set of instructions.
2. Each cell must have a full copy of all the DNA for that organism.

It takes place during interphase (not dividing and the DNA is coiled up) of the cell cycle. In eukaryotes, this results in each chromosome having an identical copy of itself (forming sister chromatids).

Question 24

Why is DNA replication semi-conservative?

Answer 24

Each DNA molecule consists of one conserved strand and one newly-built strand.

Question 25

Describe mutations, regarding DNA replication.

Answer 25

During DNA replication, errors may occur – wrong nucleotide inserted. But during replication, there are enzymes that can ‘proofread’ and edit out incorrect nucleotides, reducing the mutation rate. If a change does occur in the gene, there is a new allele (a gene in comparison to another). Mutations can be harmful, advantageous (bacteria can replicate faster), silent/neutral.

Question 26

What are genes?

Answer 26

A gene is a sequence of bases on a chromosome that codes for a particular polypeptide or protein. Genetic code is within each gene – three bases (triplet), codon, code for one amino acid.

Question 27

Describe the nature of genetic code.

Answer 27

1. Universal - in almost all living organisms, the same triplet of DNA bases, codes for the same amino acid 2. Degenerate - for all amino acids (except methionine/tryptophan), there is more than one base triplet – 64 amino acid combinations but only 20 amino acids. This is advantageous as if there is a mutation, it is less likely that it will affect the code. 3. Non-overlapping - read from a fixed starting point in groups of three bases. If a base is added or deleted (mutation), a ‘frame shift’ of every base triplet, after that, changes.

Question 28

What are the forms of RNA?

Answer 28

1. mRNA (messenger RNA) - made as a strand complementary to one strand of DNA – TEMPLATE strand. A copy of the other DNA strand of the double helix – CODING strand – is made and taken out of the nucleus and to the ribosome. 2. rRNA (ribosomal RNA) - along with proteins, forms ribosomes as well 3. tRNA (transfer RNA) - carries amino acids to the ribosomes where they are bonded together to form polypeptides.

Question 29

Briefly describe protein synthesis.

Answer 29

Protein synthesis has two stages – transcription and translation. Transcription – where a mRNA molecules made from a template strand of DNA, the mRNA then leaves the nucleus. Translation – where the amino acids are assembled into a polypeptide chain on a ribosome.

Question 30

Describe transcription in protein synthesis.

Answer 30

1. RNA POLYMERASE binds to a promoter sequence 2. RNA POLYMERASE unwinds the DNA – breaking hydrogen bonds between complementary bases 3. RNA POLYMERASE reads the template strand in the 3’ to 5’ direction 4. Activated (phosphorylated) RNA nucleotides bind with hydrogen bonds to their complementary bases on the template strand 5. The two extra phosphate groups on the nucleotides are released, releasing energy for bonding adjacent nucleotides 6. The mRNA strand produced in complementary to the nucleotide base sequence on the DNA template strand 7. The mRNA strand produced is a copy of the coding strand on the DNA 8. The end of transcription is signalled by a particular triplet of bases that signifies ‘stop’ (termination) 9. The mRNA is released from the DNA and passes out of the nucleus 10. The mRNA binds to a ribosome for translation to occur 11. Each three bases on the mRNA (codon) codes for a particular amino acid

Question 31

Describe translation in protein synthesis.

Answer 31

1. A molecule of RNA binds to a ribosome 2. Two codons are attached to the small subunit and exposed to the large subunit 3. The first exposed mRNA codon is always AUG – start codon 4. A tRNA with the anticodon UAC and the amino acid, methionine, forms a hydrogen bond with this codon 5. A second tRNA, carrying a different amino acid, binds to the second exposed codon with its complementary anticodon 6. A peptide bond forms between the two amino acids 7. The ribosome moves along the mRNA exposing the next codon 8. A third tRNA bring another amino acid 9. The first tRNA leaves and is able to collect and bring another of its amino acids 10. The polypeptide chain grows until a stop codon is reached.

Question 32

Describe the role of RNA polymerase in protein synthesis.

Answer 32

Binds to a promoter sequence on the chromosome – tells the enzyme where to begin transcription and which strand to transcribe. A promoter reads in a particular direction and so orients the RNA polymerase so it uses the correct strand as the template. Transcription factors (proteins) help direct RNA polymerase onto the promoter – determines which gene is expressed at what time. Reads the strand in a 3’ to 5’ direction.

Question 33

Describe the structure of ribosomes and its relevance to protein synthesis.

Answer 33

Assembled in the nucleolus (eukaryotes) from rRNA and protein. Made of two subuntis – with a groove for the mRNA to fit in. Ribosomes can move along mRNA, which slides through the groove.

Question 34

Describe the structure of tRNA and its relevance to protein synthesis.

Answer 34

The RNA folds into a hairpin shape. Made in the nucleus. Passes into the cytoplasm. At one end are three exposed bases, where an amino acid can bind. At the other end: three exposed bases – the anticodon can bind temporarily with its complementary codon..

Question 35

What is the importance of amino acids?

Answer 35

The sequence forms the primary structure of a protein, which determines the tertiary structure (3D) – held by hydrogen/disulphide etc. bonds. The tertiary structure is what allows the protein to function so if its altered the protein can no longer function – the shape of an active site changes.

Question 36

Define ATP.

Answer 36

ATP is energy rich and a product of respiration.

Question 37

Define phophorylated.

Answer 37

Have extra phosphate groups – are not bonded to anything in the nucleus.

Question 38

Define codon.

Answer 38

Three mRNA bases and codes for one amino acid.

Question 39

Define anticodon.

Answer 39

Three tRNA bases that are complementary to a codon.