Topic 6 Nucleic Acids and Protein Synthesis.

Question 1

What are the two key features of a DNA molecule in terms of its abilities?

Answer 1

• The ability to store information: the information needed is a set of instructions for controlling the behaviour of cells.
• The ability to copy itself accurately: whenever a cell divides it must pass on exact copies of the ‘genetic molecule’ to each of its daughter cells so no information is lost.

Question 2

What is DNA and RNA?

Answer 2

DNA (which stands for deoxyribonucleic acid) and RNA (which stands for ribonucleic acid) are polynucleotides (polymer), made up of long chains of nucleotides (monomer).

Question 3

What is the name of the bond that connects adjacent monomers after condensation?

What is the bond that links adjacent base pairs?

Answer 3

The bond between adjacent monomers after condensation is called a phosphodiester bond (a type of covalent bond).

The bond between adjacent base pairs in DNA is called a hydrogen bond.

Question 4

What is a nucleotide?

Answer 4

A molecule consisting of a nitrogen-containing or nitrogenous base, a pentose sugar molecule (which is a five carbon sugar and can be either ribose in RNA or deoxyribose in DNA) and a phosphate (PO₄³⁻) group.

The phosphate (PO₄³⁻) group is negatively charged, making DNA and RNA negatively charged molecules.

Question 5

How are polynucleotides formed?

Answer 5

Polynucleotides are formed through the process of polymerisation, where individual nucleotides are joined together during condensation reactions forming long chains.

This process is catalyzed by enzymes known as DNA polymerases or RNA polymerases, depending on whether DNA or RNA is being synthesised.

The nucleotides are linked together through phosphodiester bonds, which connect the sugar of one nucleotide to the phosphate group of the next, forming a backbone for the polynucleotide chain.

Question 6

What is a phosphodiester bond?

Answer 6

A phosphodiester bond is a bond joining two nucleotides together. The phosphate group involved now has two ester bonds, one of each of the sugars it is connected to.

Question 7

What are the four different nitrogen-containing/ nitrogenous bases found in DNA?

Answer 7

In DNA the bases are:
- Adenine.
- Guanine.
- Thymine.
- Cytosine.

Question 8

What are the four different nitrogen-containing/ nitrogenous bases found in RNA?

Answer 8

In RNA the bases are:
- Adenine.
- Guanine.
- Uracil.
- Cytosine.

Question 9

What are purines and pyrimidines?

Answer 9

Adenine and guanine contain double ring structures and are classified as purine bases.

Thymine, uracil and cytosine contain single ring structure and are classified and pyrimidines.

NOTE THAT: Purine always binds with pyrimidine.

Question 10

What are the main structural differences between DNA and RNA?

Answer 10

• Strands:
  - DNA is typically double-stranded, forming a double helix structure.
  - RNA is usually single-stranded.
• Sugar:
  - DNA contains deoxyribose sugar.
  - RNA contains ribose sugar (contains 1 oxygen atom more than deoxyribose).
• Nitrogenous Bases:
  - DNA has A, T, C, and G.
  - RNA has A, U, C, and G.

Question 11

What is adenosine triphosphate (ATP)?

Answer 11

Adenosine triphosphate (ATP) is an energy-carrying molecule found in the cells of all living things formed from the process of cellular respiration in the mitochondria of a cell and is released it to fuel other cellular processes.

Question 12

What is the structure of ATP?

Adenosine can also be combined with 1 and 2 phosphate groups. Name them.

Answer 12

ATP or adenosine triphosphate is a nucleotide that consists of three main structures: the nitrogenous or nitrogen-containing base (adenine), the pentose sugar (ribose) and a chain of three phosphate groups.

Adenosine monoposphate, adenosine diphosphate respectively.

Question 13

What are three functions of ATP?

Answer 13

• Metabolic reactions.
• Transporting substances across membranes against their concentration gradients such as in active transport.
• Energy needed for mechanical work in cells such as cell motility.

Question 14

Describe the structure of DNA and RNA.

Answer 14

• DNA and RNA have a sugar-phosphate backbone. In DNA, the sugar is deoxyribose, while in RNA, it is ribose. The sugar molecule has a five-carbon structure.
• Each sugar is attached to a phosphate group, which connects to the next sugar in the chain through a phosphodiester bond (strong covalent bond). This bond forms when the hydroxyl group of the sugar reacts with the phosphate group.

In DNA only:
- The antiparallel nature of DNA means that its two strands run in opposite directions, with one strand going from 5’ to 3’ and the other from 3’ to 5’.

Question 15

Explain the complementary base pairs in DNA and RNA, focusing on the number of hydrogen bonds formed?

Answer 15

Complementary base pairing occurs between opposite strands.

The number of hydrogen bonds between complementary base pairs is as follows:
- A and T are connected by 2 hydrogen bonds.
- C and G are connected by 3 hydrogen bonds.
- In RNA, A pairs with U through 2 hydrogen bonds.

This difference in hydrogen bonding contributes to the stability of the DNA double helix, with C-G pairs being stronger due to the three bonds compared to the A-T pairs.

Question 16

Why are hydrogen bonds essential to the structure of nucleic acids?

4 reasons.

Answer 16

• Hydrogen bonds provide stability to the DNA double helix and the structure of RNA.
• The presence of hydrogen bonds allows the double helix to be flexible, which is important for the unwinding of DNA during replication and transcription.
• The specific pairing of bases (A with T/U and C with G) via hydrogen bonds ensures accurate base pairing.
• Hydrogen bonds also can easily reform without chemical reaction.

NOTE THAT: Hydrogen bonds are relatively weak compared to covalent bonds.

Question 17

Describe semi-conservative DNA replication.

Answer 17

Semi-conservative DNA replication is the process by which DNA makes a copy of itself. This occurs in the nucleus of the cell during S phase of interphase.

Question 18

Why is DNA replication described as semi-conservative?

Answer 18

DNA replication is called semi-conservative because each new DNA molecule contains one original strand and one newly synthesized strand, where the strands from the original DNA molecule act as templates.

Question 19

What substances are needed for semi-conservative DNA replication?

Answer 19

• Helicase: This enzyme unwinds and separates the double-stranded DNA to allow replication to occur.
• DNA Polymerase: This enzyme synthesizes new DNA strands by catalysing the formation of phosphodiester bonds.
• DNA Ligase: An enzyme that catalyses the joining of two nucleotides with covalent phosphodiester bonds.
• Requires ATP.

Question 20

Explain the process of semi-conservative DNA replication?

Answer 20

Semi-conservative replication of DNA involves several key steps:

• The enzyme helicase unwinds the double helix by breaking the hydrogen bonds, separating the two strands of DNA which will be used as templates.
• DNA polymerase adds nucleotides held by hydrogen bonding to the complementary template strand being copied in a 5’ to 3’ direction extending the new DNA strand. This occurs continuously on the leading strand and in short segments (Okazaki fragments) on the lagging strand.
• DNA ligase joins the Okazaki fragments on the lagging strand, sealing any gaps in the sugar-phosphate backbone by synthesising the formation of phosphodiester bonds.

This results in 2 DNA molecules each containing 1 original strand and 1 newly synthesised strand.

Question 21

What distinguishes the leading strand from the lagging strand in DNA replication?

Answer 21

DNA polymerase only adds nucleotides from 5’ to 3’ direction.

• As the original strand is unzipped from 3’ to 5’ end, DNA polymerase runs towards the replication fork and can synthesise the leading strand continuously.
• On the lagging strand, the DNA polymerase moves away from the replication fork and hence the strand is synthesised as short fragments called Okazaki fragments.

Question 22

How does the nucleus regulate all the activities of a cell?

Answer 22

The nucleus houses its genetic material (DNA) that contains instructions for cell functions. It turns specific DNA segments into messenger RNA (mRNA), which is then used to make proteins. The nucleus also regulates which genes are active.

Question 23

What are the stages of protein synthesis?

Answer 23

• Transcription.
• RNA processing.
• Translation.

Question 24

What is a gene?
What are the features of the genetic code?

Answer 24

A gene is a specific sequence of DNA.

The genetic code has several key features:

• Triplet Code: The code is composed of triplets of nucleotides (codons), with each codon specifying a particular amino acid.
• Universality: This means that each triplet codes for the same amino acid in all living things.
• Redundancy: Multiple codons can code for the same amino acid.
• Start and Stop Codons: Specific codons signal the beginning (start codon e.g. AUG = methionine) and end (stop codons e.g. UAA, UAG and UGA) of protein synthesis.

Question 25

What types of RNA are needed for protein synthesis? ## Footnote ***NOTE THAT:*** Protein synthesis occurs in the nucleus during G1 and G2 phase of interphase.

Answer 25

- ***Messenger RNA (mRNA)***: Carries the genetic information from DNA to the ribosome, where protein synthesis occurs. - ***Transfer RNA (tRNA)***: Made in the nucleus but found in the cytoplasm and ribosome. It brings specific amino acids to the ribosome for peptide bond formation, matching them to the corresponding codons on the mRNA. - ***Ribosomal RNA (rRNA)***: Made in the nucleolus and forms the structural and functional components of ribosomes, facilitating the translation of mRNA into proteins. - ***Additional materials*** necessary for protein synthesis are: - RNA polymerase. - Codons. - Anticodons. ## Footnote Transfer RNA (tRNA) is single stranded, but folded back on itself, forming a clover-leaf shape (3 loops).

Question 26

What are codons and anticodons?

Answer 26

- A ***codon*** is a sequence of three nucleotides in ***mRNA*** that specifies an amino acid or a stop signal in protein synthesis. - An ***anticodon*** is a sequence of three nucleotides on ***tRNA*** that is complementary to a codon in mRNA. ## Footnote Anticodons form complementary base pairs with codon mRNA at the ribosome.

Question 27

Ribosomes: - Describe the structure of the ribosomes. - What is the function of the ribosomes?

Answer 27

- Ribosomes are small, spherical organelles ***composed of ribosomal RNA (rRNA) and ribosomal proteins***. - Ribosomes are the sites of protein synthesis in the cell. They translate messenger RNA (mRNA) sequences into polypeptide chains.

Question 28

What is RNA polymerase and what role does it play in protein synthesis?

Answer 28

***RNA polymerase is an enzyme that synthesizes RNA*** (in the 5' to 3' direction) from a DNA template during transcription. It binds to DNA, unwinds it, and forms phosphodiester bonds between nucleotides in the growing RNA strand.

Question 29

Descibe the process of transcription.

Answer 29

- Transcription occurs in the ***nucleus*** and is catalysed by the ***enzyme RNA polymerase***, which binds to the gene and unwinds the DNA. Helicase helps break the hydrogen bonds between the strands, exposing two single strands. - As RNA polymerase moves along the DNA, it adds complementary RNA nucleotides, forming phosphodiester bonds to create a growing RNA strand. - Only the template strand is copied into a ***complementary RNA molecule***, while the other strand remains non-transcribed. ## Footnote This is pre-mRNA which is the unprocessed transcript synthesized from a gene during transcription. It contains both coding regions (exons) and non-coding regions (introns). The strand that is copied is called the template/transcribed strand and the other strand that is not copied is called the non-transcribed strand.

Question 30

Describe the process of RNA processing.

Answer 30

RNA processing is the modification of pre-mRNA into mature mRNA and occurs in the nucleus. Before becoming mature mRNA, pre-mRNA undergoes a process called ***splicing to remove non-coding regions called introns and join coding regions called exons***. The resulting mature mRNA is then ready for translation into protein. ## Footnote Mature mRNA leaves the nucleus via the nuclear pore.

Question 31

Describe the process of translation.

Answer 31

Translation is the process by which a sequene of bases in mRNA is converted to a sequence of amino acids in a polypeptide. - The ribosome binds to the mRNA at the start codon (AUG), where the first tRNA, carrying ***methionine***, attaches to the codon. - The ribosome moves along the mRNA, reading codons. Each tRNA anticodon brings the corresponding mRNA codon forming ***hydrogen bonds***. - A second tRNA molecule with amino acids binds with the next codon on mRNA where the amino acids are linked together by ***peptide bonds***, forming a ***polypeptide chain***. - The process continues until the ribosome reaches a ***stop codon*** (UAA, UAG, or UGA). At this point, the completed polypeptide is released. ## Footnote ***NOTE THAT:*** 2 tRNA molecules are bound at the ribosomes at a time.

Question 32

What are the two types of mutation?

Answer 32

Two types of mutations are: - ***Chromosome mutation:*** Change in the structure or number of chromosomes in a cell. - ***Gene mutation:*** A gene mutation is a change in the nucleotide base sequence in a DNA molecule that may result in an altered polypeptide.

Question 33

There are different types of gene mutation. Three of the most common are:

Answer 33

- ***Substitution:*** Replacing one nucleotide base with another. - ***Deletion:*** Removing one or more nucleotide bases from the DNA sequence. - ***Insertion:*** Adding one or more nucleotide bases into the DNA sequence.

Question 34

Outline how each of these types of mutation may affect the polypeptide produced.

Answer 34

- Substitution may lead to: - ***A silent mutation*** which is a change in the DNA sequence that does not affect the amino acid sequence of the resulting protein. - ***A nonsense mutation*** in whicha stop codon is introduced prematurely. - ***A missense mutation*** in which a different amino acid is incorporated, potentially altering the protein's function. - Deletion and insertion may lead to: - ***A frameshift mutation***, altering the reading frame of the codons usually resulting in a completely different polypeptide sequence, often leading to a nonfunctional protein.

Question 35

Give an example of a gene mutation.

Answer 35

Sickle cell anemia is caused by a specific gene mutation where a ***single nucleotide is substituted*** in the hemoglobin gene, ***changing glutamic acid to valine***. This results in abnormal haemoglobin that causes red blood cells to become rigid and sickle-shaped.