Protein synthesis and mutations

Question 1

What is a gene?

Answer 1

A length of DNA that codes for 1 or more polypeptides.

Question 2

What is the genetic code?

Answer 2

Set of rules by which the information encoded in genetic material by nucleotide bases are translated into the primary structure of a polypeptide.

Question 3

What are the characteristics of the genetic code?

Answer 3

• Triplet code: A sequence of 3 consecutive nucleotide bases along a gene codes for a specific amino acid in the polypeptide.This is called a codon
• Degenerate: There are 4 bases, so there are 64 different codons. However, there are only 20 amino acids, so not all the codons are needed. As a consequence, almost all amino acids (except methionine) are coded for by more than 1 codon.
• Some codons are ‘stop’ codons and indicate the end of a polypeptide chain during protein synthesis.
• Widespread: Most organisms have very similar genetic codes, apart from a few variations in 1 or 2 amino acids. This allows for genetic engineering to take place.

Question 4

What are the benefits of having a degenerate code?

Answer 4

• Multiple codons coding for the same amino acids usually vary by 1 base (3rd base).
• If a mutation occurs, there’s a chance it will only affect the 3rd base, the codon could still code for the same amino acid.
• This reduces the effect of mutations on genes.

Question 5

What are exons?

Answer 5

Parts of a pre-mRNA molecule that code for amino acids.

Question 6

What are introns?

Answer 6

Parts of a pre-mRNA molecule that don’t code for amino acids.

Question 7

What is the sequence of events that occur during transcription?

Answer 7

1. RNA polymerase attaches to the start of the gene to be transcribed.
2. Hydrogen bonds between the bases on the 2 DNA strands along length of gene break and the DNA unwinds.
3. Free RNA nucleotides in the nucleus pair up with the exposed nucleotides on the template DNA strand by complementary base pairing (A-U/T-A, C-G) and attach to them by hydrogen bonding. This is catalysed by RNA polymerase.
4. Free RNA nucleotides are joined together by condensation reactions between adjacent ribose and phosphate groups to form sugar-phosphate backbone. This is catalysed by RNA polymerase as it moves along the template DNA strand, until it stops and detaches when a stop codon is reached.
   5*. This forms a (pre-)mRNA molecule which is complementary to template DNA strand, a replicate of the coding strand.
5. Hydrogen bonds between (pre-)mRNA nucleotides bases and template DNA nucleotide bases break.
   7*. Pre-mRNA spliced to remove introns and form mature mRNA.
6. mRNA strand diffuses out of the nucleus through nuclear pores in nuclear envelope and enter the cytoplasm.
7. Hydrogen bonds between template and coding DNA strand nucleotides reform and DNA recoils to reform double helix.

Question 8

Why is transcription important?

Answer 8

• DNA is too big to fit through nuclear pores, but mRNA molecules aren’t and copy the genes coding for polypeptides to transfers genetic information to ribosomes outside nucleus, allowing protein synthesis.
• Many copies of mRNA can be made of 1 gene on DNA, which is important for the rapid synthesis of lots of a specific protein.

Question 9

What is transcription?

Answer 9

The creation of a single-stranded mRNA copy of the DNA strand coding for a gene.

Question 10

What is tRNA?

Answer 10

• Transfer RNA.
• Carries free amino acids in the cytoplasm to ribosomes where they are assembled into a polypeptide.
• Each tRNA molecule specific to 1 amino acid.
• Folded into hair-pin shape.
• Has 3 exposed nucleotides on one end which binds to a specific amino acid.
• On the other end, there’s 3 unpaired nucleotides complementary to the codons on mRNA coding for the amino acid attached. This is called the anti-codon.

Question 11

What is translation?

Answer 11

The assembly of a polypeptide at ribosomes in reference to primary amino acid structure determined by mRNA.

Question 12

What is the sequence of events that occur during translation?

Answer 12

1. Within cytoplasm, free amino acids become attached to specific tRNA molecules with the correct anti-codon,
2. mRNA attaches to the ribosome .
3. The first exposed codon on mRNA is always AUG, coding for amino acid methionine and acting as a start codon.
4. The tRNA molecule with anti-codon complementary to to AUG codon attaches to the codon via hydrogen bonding. This brings methionine to ribosome.
5. A second tRNA with complementary anti-codon binds to the second codon on mRNA, bringing the second amino acid.
6. Enzymes in the ribosome catalyse the condensation between methionine and second amino acid to form a peptide bond.
7. Ribosome moves along mRNA by 1 codon to read the third codon; with a third tRNA molecule binding to the codon, bringing another amino acid which attaches to the dipeptide.
8. tRNA unbinds from first AUG codon and reattaches to methionine in cytoplasm.
9. Process continues whereby ribosomes move along mRNA a codon at a time, with a tRNA leaving as another one binds. The polypeptide chain grows 1 amino acid at a time.
10. Ribosome reaches a stop codon on mRNA and drops off, stopping polypeptide chain from growing. mRNA is released, along with a newly synthesised polypeptide.

Question 13

What is the role of cyclic AMP in protein activation?

Answer 13

cAMP binds to proteins and change their 3D (tertiary) shapes. This activates them and allows them to carry out their function. E.g. the active site of an enzyme becomes complementary to the substrate and is able to catalyse reaction.

Question 14

What are mutations?

Answer 14

Change in the amount/arrangement of genetic material in cells.

Question 15

What are chromosome mutations?

Answer 15

Changes in the number/structure of chromosomes the nucleus of cells.

Question 16

What are gene mutations?

Answer 16

Changes to the sequence of nucleotide bases found in a gene.

Question 17

What factors can cause mutations?

Answer 17

• Mistakes during DNA replication before nuclear divisions (mitosis/meiosis).
• Electromagnetic radiation (e.g. x-rays, UV).
• Chemical mutagens.

Question 18

What are point/substitution mutations?

Answer 18

When one base pair is replaced by another.

Question 19

What are Insertion mutations?

Answer 19

When a base pair is added to a length of DNA. This causes a triplet frameshift affecting reading of every codon downstream from the site of insertion.

Question 20

What are deletion mutations?

Answer 20

When a base pair is removed from a length of DNA. THis causes a triplet frameshift affecting the reading of every codon downstream from the site of deletion.

Question 21

What are frameshifts?

Answer 21

When the insertion/deletion of base pairs into a sequence of DNA causes a change in the reading frame of all codons downstream from the site of mutation. This completely changes the amino acid sequence coded for by these codons.

Question 22

How can mutations affect the function of a protein?

Answer 22

• Mutations may change the primary structure (amino acid sequence) of polypeptides making up protein.
• This has an effect on the tertiary (3D) structure of the protein which may result in it not working properly.
• E.g. Active site on enzyme may no longer be complementary to substrate. Substrate-enzyme complexes cannot form, so the enzymes don’t function.

Question 23

What are silent mutations?

Answer 23

Mutations in a gene that don’t have any significant affect on the structure and function of the polypeptide/protein coded for by that gene.

Question 24

How can silent mutations occur?

Answer 24

• Point mutations in non-coding parts (introns) of a gene have no effect on the sequence of amino acids.
• Point mutation in a codon (replacing one base for another) turns it into new codon coding for same amino acid (genetic code degenerate). Primary structure of protein/polypeptide unaffected. This is called a synonymous substitution.
• Point mutation in a codon turns it into new codon coding for a different amino acid to originally, but one very similar in structure to original amino acid, so has little effect on tertiary structure and function of protein/polypeptide.

Question 25

What are nonsense mutations?

Answer 25

Point mutation in a codon turns it into a premature stop codon. This ends the polypeptide before it’s fully formed, so will have major effect on its function.

Question 26

What are missense mutations?

Answer 26

Point mutation in a codon that turns it into a new codon coding for a different amino acid to originally.

Question 27

What are example of diseases associated with mutations?

Answer 27

• Cystic fibrosis is usually caused by a deletion mutation in a gene coding for a specific polypeptide.
• Sickle-cell anaemia is caused by a point mutation on codon 6 of the gene coding for the β-polypeptide in haemoglobin; resulting in valine being substituted for glutamic acid, which has profound effect on tertiary structure of β strand.

Question 28

How can mutations have neutral effects?

Answer 28

• If the mutation is a silent mutation and does not cause significant change in structure of a protein.
• If a mutation does cause a significant change in the structure of a certain protein produced, that in turn produces a different characteristic in future generations. But if the new characteristic does not benefit or harm the organisms in any way in its current environment, then the mutation is said to have a neutral effect. An example of this are the attached/free ear lobes in humans.

Question 29

How can mutations have beneficial effects?

Answer 29

• If the mutations give rise to characteristics that are beneficial to the organism in some way and increases its chance of survival.
• E.g. some bacteria mutate and develop the alleles that allow them to produce enzymes that break down antibiotics, or another mechanism which makes them antibiotic resistance. This benefits the bacteria as it prevents the bacteria from being killed by antibiotics.

Question 30

How can mutations have harmful effects?

Answer 30

• If the mutations give rise to characteristics that are harmful to the organism in some way and decreases its chance of survival.
• Genetic diseases like cystic fibrosis are caused by mutations. They severely impact the quality of life of the people who have it and most of the time, reduce their life expectancy. These mutations are therefore harmful mutations.