2.7 - DNA replication, transcription and translation

Question 1

The replication of DNA is semi-conservative and depends on complementary base pairing

Answer 1

• When a cell prepares to divide, the two strands of the double helix separate
• Each of the original strands serves as a guide, a template for the creation of a new strand
• The new strands are formed by adding nucleotides, both composed of an original strand and newly synthesised strand  DNA replication is referred to as being semi-conservative
• The base sequence on the template determines the base sequence on the new strand
• Only a nucleotide carrying a base that is complementary to the next base on the template strand can successfully be added to the new strand
• This is because complementary bases form hydrogen bonds with each other, stabilising the structure
• If a nucleotide with the wrong base started to be inserted, hydrogen bonding between bases would not occur and the nucleotide would not be added to the chain
• The rule that one base always pairs with another is called complementary base pairing
• It ensures that the two DNA molecules that result from DNA replication are identical in their base sequences to the parent molecule that was replicated

Question 2

Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds

Answer 2

• Before DNA replication can occur, the two strands of the molecule must separate so that they can each act as a template for the formation of a new strand
• The separation is carried out by helicases, a group of enzymes that use energy from ATP  the energy is required for breaking hydrogen bonds between complementary bases
• A helicase consists of six globular polypeptides arranged in a donut shape
• The polypeptides assemble with one strand of the DNA molecule passing through the centre of the donut and the other outside it
• Energy from ATP is used to move the helicase along the DNA molecule, breaking down the hydrogen bonds between bases and parting the two strands
• Double-stranded DNA cannot be split into two strands while it is still helical
• Helicase therefore causes the unwinding of the helix at the same time as it separates the strands

Question 3

DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template

Answer 3

• Once helicase has unwound the double helix and split the DNA into two strands, replication can begin
• Each of the two strands acts as a template for the formation of a new strand, the assembly of the new strands is carried out by the enzyme DNA polymerase
• DNA polymerase always moves along the template strand in the same direction, adding one nucleotide at a time, free nucleotides with each of the four possible bases are available in the area where DNA is being replicated
• Each time a nucleotide is added to the new strand, only one of the four types of nucleotides has the base that can pair with the base at the position reached on the template strand.
• DNA polymerase brings nucleotides into the position where hydrogen bonds could form, but unless this happens and a complementary base pair is formed, the nucleotide breaks away again
• Once a nucleotide with the correct base has been brought through into position and hydrogen bonds have been formed between the two bases, DNA polymerase links it to the end of the new strand.
• This is done by making a covalent bond between the phosphate group of the free nucleotide and the sugar of the nucleotide at the existing end of the new strand
• The pentose sugar is the 3’ terminal and the phosphate group is the 5’ terminal, so DNA polymerase adds on the 5’ terminal of the free nucleotide to the 3’ terminal of the existing strand
• DNA polymerase gradually moves along the template strand, assembling the new strand with a base sequence complementary to the template strand
• It does this with a very high degree of fidelity – very few mistakes are made during DNA replication

Question 4

Transcription is the synthesis of mRNA copied from the DNA base sequence by the RNA polymerase

Answer 4

• The function of most genes is to specify the sequence of amino acids in a particular polypeptide
• Proteins often directly or indirectly determine the observable characteristics of an individual
• Two processes are needed to produce a specific polypeptide, using the base sequence of a gene  the first of these is transcription
• Transcription is the synthesis of RNA, using DNA as the template, because RNA is single stranded, transcription only occurs along one of the two strands of DNA

Question 5

Process of Transcription

Answer 5

1. The enzyme RNA binds to a site on the DNA at the start of a gene
2. RNA polymerase moves along the gene separating DNA into single strands and pairing up RNA nucleotides with complementary bases on one strand of the DNA. There is no thymine in RNA so uracil pairs in a complementary fashion with adenine
3. RNA polymerase forms covalent bonds between the RNA nucleotides
4. The RNA separates from the DNA and the double helix reforms
5. Transcription stops at the end of a gene and the completed RNA molecule is released

Question 6

The product of transcription

Answer 6

• The product of transcription is a molecule of RNA with a base sequence that is complementary to the template strand of DNA
• This RNA has a base sequence that is identical to the other strand of DNA, with one exception – there is uracil in place of thymine. So, to make an RNA copy of the base sequence of one strand of a DNA molecule, the other strand is transcribed
• The DNA strand with the same base sequence as the RNA is called the sense strand
• The other strand that acts as the template and has a complementary base sequence to both the RNA and the sense strand is called the antisense strand

Question 7

Translation is synthesis of polypeptides on ribosomes

Answer 7

• The second of the two processes needed to produce a specific polypeptide is translation
• Translation is the synthesis of a polypeptide, with an amino acid sequence determined by the base sequence of a molecule of RNA
• Translation takes place on cell structures in the cytoplasm known as ribosomes
• Ribosomes are complex structures that consist of a small and a large subunit, with binding sites for each of the molecules that take part in the translation
• The two subunits are composed of RNA molecules and proteins
• Part of the large subunit is the site that makes peptide bonds between amino acids, to link them together into a polypeptide

Question 8

The amino acid sequence of polypeptides is determined by mRNA according to the genetic code

Answer 8

• RNA that carries the information needed to synthesize a polypeptide is called the messenger RNA = mRNA
• The length of mRNA molecules varies depending on the number of amino acids in the polypeptide, an average length for mammals is about 2,000 nucleotides
• In the genome there are many different genes that carry the information needed to make a polypeptide with a specific amino acid sequence
• At any time a cell will only need to make some of these polypeptides
• Only certain genes are therefore transcribed and only certain types of mRNA will be available for translation in the cytoplasm
• Cells that need or secrete large amounts of a particular polypeptide make many copies of the mRNA for that polypeptide
• For Example: insulin-secreting cells in the pancreas make many copies of the mRNA needed to make insulin
• Although most RNA is mRNA, there are other types; for example; transfer RNA is involved in decoding the base sequence of the mRNA into an amino acid sequence during translation and ribosomal RNA is part of the structure of the ribosome  they are usually referred to as tRNA and rRNA

Question 9

Codons of three bases on mRNA correspond to one amino acid in a polypeptide

Answer 9

• The genetic code enables cellular machinery to convert the base sequence on the mRNA into an amino acid sequence
• There are four bases and twenty amino acids  there are sixteen combinations of two bases  living organisms use triplet code as there not enough combinations of bases to code for all twenty amino acids
• A sequence of three bases on the mRNA is called a codon, each codon codes for a specific amino acid to be added to the polypeptide
• Each codon codes for a specific amino acid to be added to the polypeptide (there are 64 possible codons)
• The three bases of an mRNA codon are designated in the table as first second and third positions
• Different codons can code for the same amino acid
• Amino acids are carried on another kind of RNA called tRNA
• Each amino acid is carried by a specific tRNA which has as three-base anticodon complementary to the mRNA codon for that particular amino acid

Question 10

Three components work together to synthesize polypeptides by translation

Answer 10

1. mRNA has a sequence of codons that specifies the amino acid sequence of the polypeptide
2. tRNA molecules have an anticodon on the mRNA and they carry the amino acid corresponding to their codon
3. ribosomes act as the binding site for mRNA and tRNAs and also catalyse the assembly of the polypeptide

Question 11

Main events of translation

Answer 11

1. an mRNA binds to the small subunit of the ribosome
2. a molecule of tRNA with an anticodon complementary to the first codon to be translated on the mRNA then binds to the ribosome
3. a second tRNA with an anticodon complementary to the second codon on the mRNA then binds. A maximum of two tRNAs can be bound at the same time
4. the ribosome transfers the amino acid carried by the first tRNA to the amino acid on the second tRNA, by making a new peptide bond. The second tRNA is then carrying a chain of two amino acids – a dipeptide
5. the ribosome moves along the mRNA so the first tRNA is released, then the second becomes the first
6. Another tRNA binds with an anticodon complementary to the next codon on the mRNA
7. The ribosome transfers the chain of amino acids carried by the first tRNA to the amino acid on the second tRNA, by making a new peptide bond
   - Stages 4 + 5 + 6 are repeated again and again, with on amino acid added to the chain each time the cycle is repeated
   - The process continues along the mRNA until a stop codon is reached, when the completed polypeptide is released
   - The accuracy of translation depends on complementary base pairing between the anticodon on each tRNA and the codon on the mRNA
   - Mistakes are very rare, so polypeptides with a sequence of hundreds of amino acids are regularly made with every amino acid correct.