Genetic Information and Variation - DNA and Protein Synthesis

Question 1

What are the different types of RNA?

Answer 1

There are a number of types of RNA. The one that transfers the DNA code from the nucleus to the cytoplasm acts as a type of messenger and is hence given the name messenger RNA (mRNA).

This mRNA is small enough to leave the nucleus through the nuclear pores and to enter the cytoplasm, where the coded information that it contains is used to determine the sequence of amino acids in the proteins which are synthesised there.

Question 2

What is a codon?

Answer 2

The term codon refers to the sequence of three bases on mRNA that codes for a single amino acid.

Question 3

What is a genome?

Answer 3

The complete set of genes in a cell, including those in mitochondria and/or chloroplasts.

Question 4

What is a proteome?

Answer 4

The full range of proteins produced by the genome. This is sometimes called the complete proteome, in which case the term proteome refers to the proteins produced by a given type of cell under a certain set of conditions.

Question 5

What is the difference between DNA and RNA?

Answer 5

DNA is composed of two nucleotide chains wound around each other (double helix). RNA is made up of a single nucleotide chain.

Question 6

What is the structure of RNA?

Answer 6

Ribonucleic acid is a polymer made up of repeating mononucleotide sub-units. It forms a single strand in which each nucleotide is made up of:

• the pentose sugar ribose
• one of the organic bases adenine, guanine, cytosine and uracil
• a phosphate group

Question 7

What are the two types of RNA that are important in protein synthesis?

Answer 7

• messenger RNA (mRNA)

- transfer RNA (tRNA)

Question 8

What is mRNA?

Answer 8

Consisting of thousands of mononucleotides, mRNA is a long single strand that is arranged in a single helix. The base sequence of mRNA is determined by the sequence of bases on a length of DNA in a process called transcription (they are complementary). There is a great variety of different types of mRNA. Once formed, mRNA leaves the nucleus via pores in the nuclear envelope and enters the cytoplasm, where it associates with the ribosomes. There it acts as a template for protein synthesis. Its structure is suited to this function because it possesses information in the form of codons (three bases that are complementary to a triplet in DNA as well as tRNA). The sequence of codons determines the amino acid sequence of a specific polypeptide that will be made.

Question 9

What is tRNA?

Answer 9

Transfer RNA (tRNA) is a relatively small molecule that is made up of around 80 nucleotides. It is a single-stranded chain folded into a clover-leaf shape, with one end of the chain extending beyond the other. This is the part of the tRNA molecule which an amino acid can easily attach. There are many types of tRNA (complementary to mRNA), each of which binds to a specific amino acid. At the opposite end of the tRNA molecule is a sequence of three organic bases, known as the anticodon. Given that the genetic code is degenerate there must be as many tRNA molecules as there are coding triplets. However, each tRNA is specific to one amino acid and has an anticodon that is specific to that amino acid.

Question 10

How can RNA join to another strand?

Answer 10

RNA can join with both DNA and other RNA molecules by complementary base pairing. The complementary base pairings that RNA forms are therefore:

• guanine with cytosine
• adenine with uracil (in RNA) or thymine (in DNA)

Question 11

What happens during protein synthesis?

Answer 11

During protein synthesis, an anticodon pairs with the three complementary organic bases that make up the codon on mRNA. The tRNA structure, with its end chain for attaching amino acids and its anticodon for complementary base pairing with the codon of the mRNA, is structurally suited to its role of lining up amino acids on the mRNA template during protein synthesis.

Question 12

Compare DNA, mRNA and tRNA.

Answer 12

DNA

1. double polynucleotide chain
2. largest molecule of the three
3. double-helix molecule
4. pentose sugar is deoxyribose
5. organic bases are adenine, guanine, cytosine and thymine
6. found mostly in the nucleus
7. quantity is constant for all cells of a species (except gametes)
8. chemically very stable

mRNA

1. single polynucleotide chain
2. molecule is smaller than DNA but larger than tRNA
3. single-helix molecule (except in a few viruses)
4. pentose sugar is ribose
5. organic bases are adenine, guanine, cytosine and uracil
6. manufactured in the nucleus but found throughout the cell
7. quantity varies from cell to cell and with level of metabolic activity
8. less stable than DNA or tRNA, individual molecules are usually broken down in cells within a few days

tRNA

1. single polynucleotide chain
2. smallest molecule of the three
3. clover-shaped molecule
4. pentose sugar is ribose
5. organic bases are adenine, guanine, cytosine and uracil
6. manufactured in the nucleus but found throughout the cell
7. quantity varies from cell to cell and with level of metabolic activity
8. chemically more stable than mRNA but less stable than DNA

Question 13

What does the protein that is manufactured depend on?

Answer 13

Exactly which proteins the biochemical machinery in the cytoplasm of each cell manufactures depends upon the instructions that are provided, at any given time, by the DNA in the cell’s nucleus.

Question 14

What is the basic process of manufacturing a polypeptide chain?

Answer 14

1. DNA provides the instructions in the form of a long sequence of bases.
2. A complementary section of part of this sequence is made in the form of a molecule called pre-mRNA - a process called transcription.
3. The pre-mRNA is spliced to form mRNA.
4. The mRNA is used as a template to which complementary tRNA molecules attach and the amino acids they carry are linked to form a polypeptide - a process called translation.

Question 15

What is transcription?

Answer 15

Transcription is the process of making pre-mRNA using part of the DNA as a template.

1. An enzyme (DNA helicase) acts on a specific region of the DNA causing the two strands to separate and expose the nucleotide bases in that region. This is because the enzyme causes the hydrogen bonds between the complementary bases to break.
2. The nucleotide bases on one of the two DNA strands, known as the template strand (antisense strand), pair with their complementary nucleotides from the pool which is present in the nucleus. The free nucleotides line up by complementary base pairing and adjacent nucleotides are joined by phosphodiester bonds. The enzyme RNA polymerase then moves along the strands and joins the nucleotides together to form a pre mRNA molecule.
3. In this way an exposed guanine base on the DNA binds to the cytosine base of a free nucleotide. Similarly, cytosine links to guanine, and thymine joins to adenine. The exception is adenine, which links to uracil rather than thymine.
4. As the RNA polymerase adds the nucleotides one at a time to build a strand of pre-mRNA, the DNA strands rejoin behind it. As a result, only about 12 base pairs on the DNA are exposed at any one time.
5. When the RNA polymerase reaches a particular sequence of bases on the DNA that it recognises as a ‘stop’ triplet code, it detaches, and the production of pre-mRNA is then complete.

Question 16

How does transcription differ between prokaryotic and eukaryotic cells?

Answer 16

In prokaryotic cells, transcription results directly in the production of mRNA from DNA as there are no introns in bacteria. In eukaryotic cells, transcription results in the production of pre-mRNA, which is then spliced to form mRNA. Hence, when inserting DNA into bacteria, you must first remove the introns because bacteria don’t know how to splice.

Question 17

What is splicing?

Answer 17

The DNA of a gene eukaryotic cell is made up of sections called exons (expressed DNA) that code for proteins and sections called introns (intervening DNA) that do not. These intervening introns would prevent the synthesis of a polypeptide.

In the pre-mRNA of eukaryotic cells, the base sequences corresponding to the introns are removed and the functional exons are joined together during a process called splicing. As most prokaryotic cells do not have introns, splicing of their DNA is unnecessary.

Question 18

What happens after the mRNA molecules get spliced?

Answer 18

The mRNA molecules are too large to diffuse out of the nucleus and so, once they have been spliced, they are released from the chromosome. It travels to the edge of the nucleus where it will gain access to the cytoplasm through a tiny hole called a nuclear pore. In prokaryotic cells, there is no nucleus, and the chromosomes are in direct contact with the cytoplasm. Outside the nucleus, the mRNA is attracted to the ribosomes to which it becomes attached, ready for the next stage of the process: translation.

Question 19

How many tRNAs are there?

Answer 19

There are about 60 different tRNAs. A particular tRNA has a specific anticodon and attaches to a specific amino acid. Each amino acid therefore has one or more tRNA molecules, with its own anticodon of bases.

Question 20

How is a polypeptide synthesised (translation)?

Answer 20

1. A ribosome becomes attached to the starting codon at one end of the mRNA molecule.
2. The tRNA molecule with the complementary anticodon sequence moves to the ribosome and pairs up with the codon on the mRNA. This tRNA carries a specific amino acid.
3. A tRNA molecule with a complementary anticodon pairs with the next codon on the mRNA. This tRNA molecule carries another amino acid.
4. The ribosome moves along the mRNA, bringing together two tRNA molecules at any time, each pairing up with the corresponding two codons on the mRNA.
5. The two amino acids on the tRNA are joined by a peptide bond using an enzyme (ATP hydrolase) and ATP which is hydrolysed to provide the required energy.
6. The ribosome moved on to the third codon in the sequence on the mRNA, thereby linking the amino acids on the second and third tRNA molecules.
7. As this happens, the first tRNA is released from its amino acid and is free to collect another amino acid from the amino acid pool in the cell.
8. The process continues in this way, with up to 15 amino acids being added each second, until a polypeptide chain is built up.
9. Up to 50 ribosomes can move along the same strand of mRNA behind one another so that several proteins can be assembled simultaneously.
10. The synthesis of a polypeptide continues until a ribosome reached a stop codon. At this point, the ribosome, mRNA and the last tRNA molecule all separate and the polypeptide chain is complete.

Question 21

What is the role of ATP in translation?

Answer 21

ATP has two roles in translation. It is required to provide energy to attach amino acids to tRNA and also to attach amino acids together.

Question 22

What determines the sequence of codons?

Answer 22

The DNA sequence of triplets that make up a gene determine the sequence of codons on mRNA.

Question 23

What determines the order in which tRNA molecules line up?

Answer 23

The sequence of codons on mRNA determine the order in which the tRNA molecules line up.

Question 24

What determines the sequence of amino acids in the polypeptide?

Answer 24

The order in which tRNA molecules line up determine the sequence of amino acids in the polypeptide. In this way genes precisely determine which proteins a cell manufactures. As many of these proteins are enzymes, genes effectively control the activities of cells.

Question 25

How is a protein assembled?

Answer 25

Sometimes a single polypeptide chain is a functional protein. Often, a number of polypeptides are linked together to give a functional protein (quaternary structure). What happens to the polypeptide next depends upon the protein being made, but usually involves the following:

• the polypeptide is coiled or folded, producing its secondary structure
• the secondary structure is folded, producing its tertiary structure
• different polypeptide chains, along with any non-protein groups, are linked to form the quaternary structure

Question 26

What are the features of the genetic code?

Answer 26

• non-overlapping
• genes are separated by non-coding repeats of bases
• degenerate
• contains start and stop codons

Question 27

What are the two stages of protein synthesis?

Answer 27

Transcription which occurs in the nucleus and involves DNA and mRNA, and translation which involves mRNA, tRNA and ribosomes. During transcription, a section of a DNA strand is transcribed into mRNA which is then translated into a polypeptide chain formed of amino acids.

Question 28

What is the difference between the genes in transcription vs translation in terms of direction?

Answer 28

transcription: promotor region -> termination sequence
translation: start codon -> stop codon

Question 29

What is the difference between non-coding DNA and introns?

Answer 29

Non-coding DNA is found between genes, introns are found within genes.

Question 30

Why is DNA helicase needed in DNA replication but not in transcription?

Answer 30

RNA polymerase does the job.

Question 31

What is the difference between the sense and antisense strand?

Answer 31

The sense strand has the information that would be readable on the RNA, and that’s called the coding side. The antisense is the non-coding strand, but when you’re making RNA, the proteins that are involved in making RNA read the antisense strand in order to create a sense strand for the mRNA.

Question 32

What are snRNPs?

Answer 32

snRNP (“snerps”) cut at splicing sites at the ends of the introns and join the exons together. This happens inside of a spliceosome. The intron that is removed is called the excised intron.

Question 33

How many proteins can one gene code for?

Answer 33

One gene can code for more than one protein depending on which sections of DNA are spliced together.

Question 34

What are ribosomes made of?

Answer 34

Ribosomes are made up of a complex of ribosomal RNA (rRNA) and proteins. They exist as two separate sub-units until they are attracted to a binding site on the mRNA molecule, when they join together.

Question 35

What are the benefits of having introns?

Answer 35

introns can provide a source of new genes