Nucleic Acid and Protein Synthesis

What three components must be present for a molecule to be classified as a nucleotide?

A phosphate group, a pentose sugar and a nitrogenous base.

Why are nucleotides able to form long polynucleotide chains?

They can join by condensation reactions, forming phosphodiester bonds between adjacent nucleotides.

What bond forms the sugar-phosphate backbone of DNA?

Phosphodiester bonds.

Why is a DNA strand described as having a 3′ end and a 5′ end?

The nucleotides are arranged with directionality based on the carbon atoms of the pentose sugars, so the two ends of the strand are chemically different.

Why are phosphodiester bonds important to DNA structure?

They form strong covalent bonds that link nucleotides together, creating the sugar-phosphate backbone of each DNA strand.

Which nitrogenous bases are purines, and what structural feature do they share?

Adenine and guanine; both have a double-ring structure.

Which nitrogenous bases are pyrimidines, and what structural feature do they share?

Cytosine, thymine and uracil; all have a single-ring structure.

Why can adenine pair with thymine in DNA but adenine pair with uracil in RNA?

DNA contains thymine instead of uracil, whereas RNA contains uracil instead of thymine

How many hydrogen bonds form between adenine and thymine?

two

How many hydrogen bonds form between guanine and cytosine?

Three

Why are the two DNA strands described as complementary?

Each base pairs specifically with its complementary base: A with T and C with G.

Why are DNA strands described as antiparallel?

The two strands run in opposite directions: one runs 5′ → 3′ and the other runs 3′ → 5′.

A DNA molecule has a high proportion of guanine and cytosine. What can you predict about the number of hydrogen bonds between its strands?

It will have more hydrogen bonds because each G-C base pair forms three hydrogen bonds.

Why might DNA with a higher G-C content require more energy to separate its strands?

G-C pairs have three hydrogen bonds, compared with two in A-T pairs, so more bonds must be broken.

What does the name adenosine triphosphate tell you about the structure of ATP?

It contains adenosine, made from adenine and ribose, and three phosphate groups

Why is ATP classified as a nucleotide derivative?

It contains a nitrogenous base, ribose sugar and phosphate groups.

During which phase of the cell cycle does DNA replication occur?

S phase of interphase.

What does semi-conservative replication mean?

Each new DNA molecule contains one original parental strand and one newly synthesised strand.

Why is each original DNA strand able to act as a template during replication?

Complementary base-pairing rules determine which nucleotides can be added to form the new strand.

What is the role of DNA helicase in replication?

It breaks the hydrogen bonds between complementary bases, causing the DNA double helix to unwind and separate.

What would happen to DNA replication if helicase could not function?

The two DNA strands could not separate properly, so they would not be available as templates for new complementary strands.

What is the role of DNA polymerase?

It adds complementary nucleotides and catalyses the formation of phosphodiester bonds, building the new DNA strand.

Why can DNA polymerase only synthesise a new strand in the 5′ → 3′ direction?

DNA polymerase can only add nucleotides to the appropriate end of a growing strand, giving synthesis a 5′ → 3′ direction.

Why is DNA replication more complicated on one of the antiparallel template strands?

Because DNA polymerase can only synthesise DNA in the 5′ → 3′ direction, one new strand must be produced discontinuously as fragments.

What are Okazaki fragments?

Short sections of newly synthesised DNA produced discontinuously on one strand during DNA replication.

Why are Okazaki fragments necessary?

DNA polymerase can only synthesise DNA in the 5′ → 3′ direction, while the two DNA template strands run antiparallel

What is the role of DNA ligase during replication?

It joins Okazaki fragments by forming phosphodiester bonds.

A mutation prevents DNA ligase from functioning. What would happen during DNA replication?

Okazaki fragments would not be joined together, leaving one newly synthesised DNA strand discontinuous.

A DNA molecule is replicated once. How many DNA molecules result, and what does each contain?

Two DNA molecules, each containing one original strand and one newly synthesised complementary strand.

Why does semi-conservative replication help ensure genetic continuity?

Complementary base pairing allows each original strand to guide formation of an accurate new complementary strand.

An enzyme breaks hydrogen bonds between DNA bases but does not form phosphodiester bonds. Identify the enzyme.

DNA helicase.

An enzyme joins adjacent DNA fragments by forming phosphodiester bonds. Identify the enzyme.

DNA ligase.

An enzyme adds nucleotides to form a new DNA strand and catalyses phosphodiester bond formation. Identify the enzyme.

DNA polymerase.

A scientist inhibits hydrogen-bond breaking in DNA before replication. Which stage of replication is directly prevented?

Separation of the two DNA strands to expose the template strands.

What are two major structural differences between RNA and DNA?

RNA contains ribose instead of deoxyribose and uracil instead of thymine. RNA is generally single-stranded.

Why can RNA contain uracil instead of thymine?

Uracil is the pyrimidine base used in RNA that pairs with adenine.

Which three bases are found in both DNA and RNA?

Adenine, cytosine and guanine.

Which base is found in DNA but not RNA, and which is found in RNA but not DNA?

Thymine is found in DNA, while uracil is found in RNA.

Why is mRNA essential for protein synthesis?

It carries genetic information from DNA to the ribosome and provides the sequence of codons used as the template during translation.

Why does each tRNA have both an anticodon and a specific amino acid attached?

The anticodon pairs with a complementary mRNA codon, ensuring the correct amino acid is brought into the growing polypeptide.

What would happen if a tRNA had an anticodon that did not complement the mRNA codon?

It would not bind correctly to that codon, so it would not add its amino acid at that position.

What is the main role of rRNA?

It is a major component of ribosomes, where protein synthesis occurs.

A cell is producing large amounts of protein. Which organelle structure would you expect to contain large amounts of rRNA?

Ribosomes.

How does a gene influence the structure of a protein?

The sequence of DNA bases determines the sequence of mRNA codons, which determines the sequence of amino acids in the polypeptide.

Why is the genetic code described as a triplet code?

Three nucleotide bases form one codon.

How many possible codons can be formed using four different bases?

64, because 4³ = 64.

Why can 64 codons code for only 20 amino acids?

The genetic code is degenerate, meaning more than one codon can code for the same amino acid.

What does it mean that the genetic code is universal?

The same codons generally code for the same amino acids in different organisms.

Why does the universal nature of the genetic code provide evidence for common ancestry?

Different organisms use essentially the same coding system, suggesting they inherited it from a common ancestor.

A mutation changes one codon but the same amino acid is still added. How is this possible?

The genetic code is degenerate, so different codons can code for the same amino acid.

Where does transcription occur in a eukaryotic cell?

In the nucleus.

What is produced during transcription?

An RNA molecule; for protein-coding genes, this is initially a primary RNA transcript/pre-mRNA that is processed to form mature mRNA.

Why must the DNA strands separate during transcription?

One strand must be exposed so it can act as a template for complementary RNA nucleotides.

What is the role of RNA polymerase during transcription?

It catalyses formation of phosphodiester bonds between RNA nucleotides, producing an RNA strand complementary to the DNA template.

In which direction does RNA polymerase read the DNA template strand?

3′ → 5′

In which direction is the RNA strand synthesised?

5′ → 3′.

Why are the template DNA strand and newly formed mRNA complementary?

RNA nucleotides pair with complementary bases on the template strand according to base-pairing rules.

What happens to the DNA molecule after transcription of a gene is complete?

The RNA detaches and the two DNA strands re-form hydrogen bonds and return to the double helix.

Why can mRNA leave the nucleus while DNA normally remains there?

mRNA carries a copy of the genetic information through nuclear pores to ribosomes, while DNA remains protected in the nucleus.

What is the difference between an intron and an exon?

Introns are non-coding sequences removed from the primary transcript, while exons are retained and joined together in the mature mRNA.

Why must RNA splicing occur before a mature mRNA molecule is translated?

Introns are removed and the remaining exons are joined to produce the correct coding sequence.

A mutation prevents introns from being removed from pre-mRNA. What could happen to the resulting protein?

The mRNA sequence could contain incorrect non-coding sequences, potentially altering codons and producing an abnormal polypeptide.

Which contains both introns and exons: DNA, pre-mRNA or mature mRNA?

DNA and pre-mRNA contain both introns and exons; mature mRNA contains the joined exons.

Where does translation occur?

At ribosomes in the cytoplasm or on the rough endoplasmic reticulum

Why must an mRNA codon pair specifically with a complementary tRNA anticodon?

This ensures the correct tRNA, carrying the correct amino acid, is selected according to the genetic code.

How does the sequence of codons in mRNA determine the sequence of amino acids in a protein?

Each codon pairs with a specific tRNA anticodon, and each tRNA carries a particular amino acid, so the order of codons determines the order of amino acids.

What bond joins adjacent amino acids during translation?

A peptide bond.

What happens to a tRNA molecule after it has transferred its amino acid to the growing polypeptide?

It leaves the ribosome and can be reused.

Why does the ribosome move along the mRNA during translation?

It reads successive codons, allowing tRNAs carrying the corresponding amino acids to bind and extend the polypeptide chain.

What causes translation to stop?

The ribosome reaches a stop codon, terminating synthesis of the polypeptide.

A mutation changes the sequence of mRNA codons. Explain how this could change the protein produced.

Different codons may pair with different tRNA anticodons, causing different amino acids to be added. This changes the primary structure and may alter the protein's shape and function.

Put these processes in the correct order: transcription, translation and RNA splicing.

ranscription → RNA splicing → translation

Explain the complete information pathway from a gene to a polypeptide. (7 steps)

DNA base sequence → transcription produces pre-mRNA → introns are removed during RNA splicing → mature mRNA leaves the nucleus → translation at a ribosome → codons pair with tRNA anticodons → amino acids are joined by peptide bonds to form a polypeptide.

Why can a change in the DNA base sequence potentially affect a protein's function?

DNA sequence changes can alter mRNA codons, changing the amino-acid sequence. This may alter the polypeptide's primary structure, folding, 3D shape and therefore its function.

What is a gene mutation?

A change in the sequence of nucleotide bases in DNA.

How can radiation or chemicals such as those in tobacco increase mutation rate?

They can act as mutagens that increase the chance of changes occurring in the DNA base sequence.

What is a substitution mutation?

One nucleotide base is replaced by a different nucleotide base.

What is a deletion mutation?

One or more nucleotide bases are removed from the DNA sequence.

What is an insertion mutation?

One or more nucleotide bases are added to the DNA sequence.

Why can an insertion or deletion cause a frameshift mutation?

If the number of bases added or removed is not a multiple of three, the grouping of bases into codons changes from that point onwards.

Why can a frameshift mutation have a greater effect than a substitution mutation?

A frameshift can change every codon after the mutation, potentially altering many amino acids, whereas a substitution usually affects only one codon.

Why does a substitution mutation not always change the amino acid sequence?

Because the genetic code is degenerate, so the altered codon may still code for the same amino acid.

Why does changing the amino-acid sequence potentially alter a protein's function?

Different amino acids have different R groups, which can alter bonding and interactions during folding, changing the protein's 3D structure and function.