2.1.3: Nucleotides + Nucleic Acids

Question 1

Describe the structure of a nucleotide

Answer 1

It is made out of 3 components:
1. A pentose monosaccharide (sugar), containing 5 carbon atoms
2. A phosphate group, PO4 2-, an inorganic molecule that is acidic and negatively charged
3. A nitrogenous base, a complex organic molecule containing one or two carbon rings in its structure as well as nitrogen

Question 2

What is a nucleotide?

Answer 2

the monomer from which nucleic acids are made

Question 3

Compare purines and pyrimidines and how to remember them

Answer 3

They are nitrogenous bases that make up the two different nucleotides in DNA and RNA.

Purine bases- They have two carbon rings to their structure (double ringed). Adenine and guanine are purine bases
Pyrimidine bases- They have one carbon ring to their structure (single ringed).

How to remember the difference
* To remember how many rings each has: Purine has a u in it and so does double ringed to purine is double ringed and pyrimidine is single ringed
* To remember which nitrogenous bases are which type:* Cytosine and Thymine both have a y in them and so does pyrimidine*

Question 4

Describe the structure of DNA

Answer 4

It is made up of:
1. 2 polynucleotide strands which are antiparallel
2. Each strand has alternating deoxyribose sugars and phosphate groups bonded together with covalent phosphodiester bonds to form the sugar-phosphate backbone
3. The phosphodiester bonds link 5-C of one sugar to the phosphate group of the same nuclotide, which is linked by a phosphodiester bond to the 3-C of the next sugar on the next nucleotide
4. Each polynucleotide strand has a 3’ and a 5’ end- one strand is the 5’ to 3’ strand and one is the 3’ to 5’ strand (due to running antiparallel)
5. There is complementary base pairing (A-T and C-G) which are held together by hydrogen bonds. A-T are held by 2H bonds and C-G are held by 3H bonds
6. It is a 3D **double helix ** shape

Question 5

Compare the structure of DNA and RNA

Answer 5

1. Sugar: DNA contains deoxyribose whereas RNA contains ribose (deoxyribose has 1 less oxygen than ribose)
2. Purine organic bases: Both contain adenine and guanine
3. Pyrimidine Organic bases: DNA contains cytosine and thymine but RNA contains cytosine and uracil
4. Number of strands: DNA contains two strands (double) but RNA contains 1 strand (single)
5. Inorganic component: Both contain a phosphate group
6. Length: RNA strands are shorter than DNA strands
7. Location: DNA is found in the nucleus (and a small amount in mitochondria) but RNA forms in the nucleus then moves to different areas depending on type

Question 6

Adaptations of the DNA molecule to its function

Answer 6

1. Stability: It is a stable molecule, held together by strong covalent bonds not easily broken down. Forming the sugar phosphate backbone and attatching to organic bases
2. Stability: The hydrogen bonds (that are easily broken to allow replication and proteinsynthesis) are protected by being on the inside of the molecule, ie the two strong **sugar phosphate backbones **give protection to the base sequence from any interference. This adds stability as the hydrogen bonds are the weakest bonds but are proteted.
3. Copy Accurately: It is able to copy itself accurately because of the complimentary pairing of the organic bases
4. Effective storage: The long DNA molecule is capable of folding itself up, so a large amount of information can be stored in a small volume, by being wound around histone proteins into chromosomes inside the nucleus
5. It carries information coded in the order of the bases, which can be easily copied

Question 7

Adaptations of the RNA molecule to its function

Answer 7

1. Short: It is Single stranded so mRNA can carry a copy of the DNA code with unpaired bases exposed
2. Small:It is smaller than the DNA molecule so it can travel Small:out of the nucleus (through the nucleur pores) and move around the cell
3. It (mRNA) forms base pairs with the correct tRNA molecule to control the sequence of amino acids in a polypeptide chain

Question 8

How do you identify deoxyribose vs ribose on a diagram?

Answer 8

On the second carbon, ribose has a hydroxyl group but this is absent on the deoxyribose (there is only a hydrogen)

Question 9

Describe DNA replication (semi-conservative replication)

Answer 9

1. DNA double helix unwinds and the hydrogen bonds are broken by the enzyme helicase
2. This exposes the organic bases which are kept apart by binding proteins
3. Free nucleotides with the correct complimentary bases slot into place opposite the exposed bases on each strand
4. A and T always join togethr and G and C
5. Hydrogen bonds are formed between the bases joining the two strands together
6. DNA polymerase joins the nucleotides together, forming the phosphodiester backbone, in a continuous chain running in the 3’ to 5’ direction as it is specififc and is only complimentary to the 3’ end
7. In the other direction the DNA polymerase joins the nucleotides together in short sections (ozaki fragments)
8. The enzyme DNA ligase the links together the ozaki fragments in the 5’ to 3’ direction
9. A new strand of DNA has then been formed against each of the old strands so that two identical DNA molecules have been produced

Question 10

Identify and decscribe the roles of the enzymes involved in DNA replication

Answer 10

1. Helicase- Seperates the two DNA strands using energy from ATP
2. DNA binding proteins- Keeps the strands seperate during replication
3. DNA polymerase- In the 3’ to 5’ direction, it catalyses the polymerisation to form the polynucleotide chain. This allows the strand to be replicated continuously. In the 5’ to 3’ direction it catalyses the polymerisation to form the polynucleotide chain, in small section. This is not continuous
4. DNA ligase- The ozaki fragments (piece of the polynucleotide chain) are joined together

Question 11

Why is DNA replication not perfect and what can cause mutations?

Answer 11

Errors occur due to
1. The high speed of replication
2. Spontaneous chemical ‘flip-flops’ in the bases

Mutations can be caused by
1. Spontaneous errors in DNA replication or meiotic recombination
2. Radiation, viruses and mutagenic chemicals
3. The organism iself by cellular processes such as hypermutilation

Question 12

Describe the three theories of DNA replication

Answer 12

1. Semi-conservative- One new strand of DNA forms against each of the original strands so that each new DNA molecule is made up of one new and one original strand
2. Conservative- A completely new DNA molecule is made with two new strands and the original one stays intact
3. Dispersive replication- Part but not all of each strand of the old DNA molecule becomes part of the new ones with new and old bits scattered amongst each other

Question 13

Describe the findings of the Meselson-Stahl experiment

Answer 13

They idenftified and seperated different isotopes of nitrogen by density centrifugation.
1. Parent DNA- the DNA grown in N15 contained all heavy N15 organic bases
2. First generation- DNA grown in N14. A hybrid model was produced with both 1 light and 1 heavy strand of DNA. As no heavy DNA is produced it rules out conservative theory of replication.
3. Second generation- DNA grown in N14. A hydbrid model is maintained but a light DNA strand is also produced. This rules out dispersive replication as if that was the explanation a ingle band would have been maintained gradually getting lighter
4. Third generation- DNA grown in N14. The hybrid model is still present but the proportion of light DNA has increased relative to the proportion of hybrid DNA
5. Fourth generation- DNA grown in N14. Same results as third generation and th proportion of light DNA to hybrid has increased and will continue to increase in future generations

Question 14

Describe the structure of a molecule of ATP (Adenosine Triphosphate)

Answer 14

It is composed of:
1. A nitrogeneous base (adenosine)
2. A pentose sugar (ribose)
3. Three phosphate groups (inorganic phosphates)

Question 15

What are ADP and ATP?

Answer 15

Phosphorylated nucleotides

Question 16

Explain how ATP stores and releases energy

Answer 16

1. Energy is needed to break bonds and is released when bonds are formed
2. A small amount of energy is needed to break the relatively weak bond holding the last phosphate group in ATP
3. A large amount of energy is released when the liberated phosphate undergoes other reactions involving bond formation
4. Overall, 30.6 kJ mol-1 energy is released from the hydrolysis of ATP

Question 17

Describe how ADP is synthesised

Answer 17

ATP is hydrolysed into adenosine diphosphate (ADP and a phosphate ion which releases energy.

The hydrolysis of ATP happens in association with energy-requiring reaction. They are ‘coupled’ together and happen simultaneously

Question 18

Describe the (re)synthesis of ATP

Answer 18

A condensation reaction occurs in a process called phosphorylation.
During this the phosphate group released in the hydrolysis of ATP is reattatched to an ADP molecule, using energy released in cellular respiration.

Question 19

Describe the properties of ATP

Answer 19

1. Small- moves easily into, out of and within cells
2. Water Soluble- energy-requiring processes happen in aqueous environments
3. Releases energy in small quantities: Contains bonds between phosphates with intermediate energy- these are large enough to be useful in cellular respiration but not so large there is waste heat energy
4. Easily regenerated- Can be recharged with energy

Question 20

Describe the roles of ATP in the body

Answer 20

ATP supplies energy for the body for the following:
1. Synthesis- eg, for large molecules such as proteins
2. Transport- eg, pumping molecules or ions across cell membranes by active transport
3. Movement- eg, protein fibres in muscle cells that cause muscle contractions

Question 21

Explain the nature of the genetic code

Answer 21

• The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code
• The sequence of three bases is called a codon. This codes for an amino acid
• One codon is a start codon which ensures the codons are read ‘in frame’ (from base 1) so the genetic code is non-overlapping
• Stop codons don’t code for an amino acid but instead terminate the chain.
• Many amino acids can be coded for by more than one codon. So, the code is degenerate.
• The genetic code is widespread (almost universal) all organisms use this same code.

Question 22

Explain how a gene determines the sequence of amino acids

Answer 22

Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid (hence, it is a triplet code). The mRNA sequence is thus used as a template to assemble—in order—the chain of amino acids that form a protein.

Question 23

Explain the process of transcription

Answer 23

1. The DNA molecule ‘opens up’ using the enzyme helicase, exposing the gene to be read
2. Only 1 DNA strand contains the code for the protein to be synthesised. This is the sense strand and runs in the 5’ to 3’ direction
3. The other strand is complimentary to the sense strand. It runs in the 3’ to 5’ end and is the antisense strand
4. The antisense strand acts as a template during transcription- so, the complimentary RNA strand formed carries the same base sequence as the sense strand
5. Free RNA nucleotides, which are complimentary to C-G and A-U, bond to the exposed bases on the template strand
6. The RNA nucleotides are then joined by phosphodiester bonds using the enzyme RNA polymerase which creates the mRNA molecule which is identical to the Coding (sense) strand
7. The mRNA then peels away from the DNA strand
8. The DNA double helix can then reform
9. The mRNA strand leaves the nucleus through the nuclear pore and attatches to a ribosome which is composed of rRNA (ribosmal RNA)

Question 24

Explain the process of translation

Answer 24

1. The ribosome is made up of two subunits, one large and one small. They’re composed of protein and rNA (ribosmal RNA)
2. The mRNA binds to the small subunit of the ribosome at its start codon and is held in place until it is completely translated into a sequence of amino acids.
3. A tRNA is folded with the complimentary anticodon (the triplet code that will recognise the specific codon in mRNA) at one end
4. The tRNA binds to the mRNA start codon
5. Another tRNA with an anticodon + corresponding amino acid binds to the next codon on the mRNA. A maximum or 2 tRNAs can be bound at the same time
6. The first amino acid is transferred to the amino acid on the second tRNA by the formation of a peptide bond.
7. This is catalysed by the enzyme peptidyl transferase which is an rNA component of the ribosome
8. The ribosome then moves along the mRNA, releasing the first tRNA. The second becomes the first.
9. The stages are repeated, adding another amino acid to the chain each time, until the ribosome reaches the end of the mRNA at a stop codon and the polypeptide chain is released (this is a primary structure of a protein.

Question 25

What happens after the primary structure of the protein has been formed?

Answer 25

1. The primary structures then fold into the secondary and tertiary structures.
2. This folding and the bonds that are formed are determined by the sequence of amino acids in the primary structure.
3. The protein may unergo further modifications on the golgi apparatus before it is ready to carry out its roles