OCR Module 5 Gene Regulation

Question 1

Explain how the functions of cells are controlled by the nucleus

Answer 1

1. The functions of cells (such as metabolism) are carried out by proteins
2. The function of proteins are determined by their tertiary structure
3. The tertiary structure is dependent on the primary structure 4.The primary structure is translated from the codons of the mRNA
4. The mRNA is transcribed from the alleles of a gene in the chromosomal DNA found in the nucleus.

Question 2

Summarise how mutations can affect the function of cells

Answer 2

1. A mutation is a change in the base sequence of DNA
2. During transcription, this can cause a change in the codons of mRNA
3. Changes in mRNA codons can result in a different primary structure
4. This can change the tertiary structure of the protein (3D shape)
5. A different tertiary structure can affect the function of a protein and therefore the functioning of a cell

Question 3

Identify the types of mutation that can occur in DNA

Answer 3

• Point mutations
a. Substitutions - Code for new amino acid or due to degenerate nature, code for same amino acid.
b. Frameshift (insertion)
c. Frameshift (deletion)
• Chromosomal mutations
a. Deletion - Section of chromosome breaks off and lost in cell.
b. Duplication - Sections of chromosome are duplicated.
c. Translocation - Section breaks off and joins another non homologous chromosome.
d. Inversion - Section breaks off, is reverse and joins back.

Question 4

Explain the extent to which substitution mutations alter protein structure

Answer 4

1. Substitution is the replacement of one base with another
2. This alters one triplet in the DNA and one codon in the mRNA
3. This would change one amino acid in the polypeptide
4. However, due to the degenerate nature of genetic code
5. The new codon may still code for the same amino acid
6. This will cause no change to the protein structure, and so no effect on protein function.

Question 5

Explain the extent to which insertion mutations alter protein structure

Answer 5

1. Insertions are the addition of bases into the original DNA sequence
2. This changes the triplet where it is added, but also the reading frame from that point onwards
3. This can alter every single triplet/codon after the insertion or even introduce a premature STOP codon
4. Therefore can have a very significant effect on protein structure and function
5. However, insertions of multiples of three do not change the reading frame
6. They will only add some amino acids to the protein structure

Question 6

Explain the extent to which deletion mutations alter protein structure

Answer 6

1. deletions are the removal of bases from the original DNA sequence
2. This changes the triplet where it is occurs, but also the reading frame from that point onwards
3. This can alter every single triplet/codon after the deletion or even introduce a premature STOP codon
4. Therefore can have a very significant effect on protein structure and function
5. However, deletions of multiples of three do not change the reading frame
6. They will only remove some amino acids from the protein structure

Question 7

Describe the range of effects that mutations can have on protein function

Answer 7

1) No effect on protein structure and function
a. For example substitutions that do not affect the primary structure of the protein
2) Mutations can be damaging
a. Single amino acid changes, or frameshifts
b. Can change the protein structure so that it does not function
c. This can affect cell, tissue and even organ function
3) Beneficial
a. Changes to protein structure
b. May result in improved or new functionality (depending on the selection pressure)

Question 8

Explain what gene expression is

Answer 8

1. Gene expression is the term that describes synthesis of a protein from its gene
2. Genes are located on chromosomes in the DNA stored in the nucleus
3. For a gene to be expressed, it must first be transcribed (by RNA polymerase) to produce mRNA
4. The mRNA of the gene must then translated (by ribosomes) to produce the functional protein
5. This protein will affect the function of the cell

Question 9

Describe the advantages of regulating gene expression

Answer 9

1. The expression of genes can switched on or off
2. This allows prokaryotic cells to respond to changes in their environment
3. Allows cells to only express genes when they are needed (saving energy, resources)
4. Allows cells to express genes specific to their function (differentiation, specialisation)
5. Allows cells/tissues to make responses to chemical signals (hormones, paracrine signalling)
6. Allow gene expression to change through time, so that organisms can develop

Question 10

State the levels at which gene expression can be regulated

Answer 10

1. Transcription initiation
2. Post-transcriptional
3. Post-translational control

Question 11

Describe how mRNA splicing is a post-transcriptional gene regulatory mechanism

Answer 11

1. A gene contains coding exons, and non-coding introns
2. Transcription results in pre-mRNA which also contains exons and introns
   3 .The introns are removed and during a process called splicing, the exons are joined together to produce the final mRNA
3. At this stage, signalling can result in the exons being spliced together in different sequences (alternative splicing)
4. This produces different mRNAs, with different sequences of codons
5. Which will result in proteins with different shapes and functions being produced

Question 12

Describe how gene expression can be controlled at the post-translational level

Answer 12

1. Post-translational means after the polypeptide has been made
2. Post-translational modifications can change the activity of the protein (and therefore the characteristic determined by the gene)
3. Post-translational modifications include:
   a. Carbohydrate and lipid modifications
   b. Cutting off parts of the protein to make it active, eg zymogens to enzymes
   c. Adding and removing a phosphate group
   d. Binding of second messengers such as cyclic AM

Question 13

Describe how transcription initiation can be regulated by DNA-binding proteins

Answer 13

1. Transcription is affected by DNA binding proteins
2. These bind to the specific regulated gene through their DNA-binding domain
3. These proteins can enhance or prevent RNA polymerase from binding to gene
4. Transcription factors enhance the gene’s transcription
5. Repressor proteins inhibit the gene’s transcription
6. And so gene expression can be activated or inhibited

Question 14

Summarise the function of the Lac operon

Answer 14

1. Bacterial cells can use different sugars for respiration
2. Different genes need to be expressed to use different sugars
3. It is wasteful to express genes for the use of different sugars at the same time
4. The Lac operon is a group of genes that are activated by the presence of the sugar lactose
5. Thus ensuring that genes for lactose metabolism are only expressed when lactose is available
6. This saves energy and resources of bacterial cells

Question 15

Describe the structure of the Lac operon

Answer 15

1. The Lac operon is a stretch of DNA that contains genes required for lactose metabolism
2. The operon contains three structural genes
3. The LacY gene encodes a channel protein that allows lactose to enter bacterial cells (lactose permease)
4. The LacZ gene encodes the enzyme b-galactosidase, that hydrolyses the disaccharide lactose into glucose and galactose
5. The operon also contains the regulatory gene, LacI, which encodes a repressor protein
6. Between the regulatory and structural genes are the Promoter and Operator regions of DNA

Question 16

Describe the function of the Lac operon in the absence of lactose

Answer 16

1. In the absence of lactose the repressor protein binds the operator region
2. This prevents RNA polymerase from binding the promoter
3. lac operon structural genes are not transcribed
4. The genes for lactose metabolism are not expressed

Question 17

Describe the function of the Lac operon in the presence of lactose

Answer 17

1. In the presence of lactose, lactose binds to the repressor protein
2. This prevents the repressor from binding the operator region
3. RNA polymerase can bind the promoter
4. lac genes are transcribed and expressed
5. Lactose diffuses into bacterial cells through lactose permease
6. Lactose metabolism is initiated by b-galactosidase
7. Lactose can be used as a respiratory substrate

Question 18

Explain how and why fruitflies are used to study morphogenesis

Answer 18

1. Morphogenesis is the anatomical development of an organism.
2. Fruit flies are small, easy to maintain and have a short life cycle,.
3. Individuals with abnormal development can be easily identified.
4. Their DNA can be compared with those of normal development.
5. To identify the genes that are involved in regulating morphogenesis.

Question 19

Explain what homeobox gene are

Answer 19

1. DNA sequence, around 180 base pairs long, found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi and plants
2. When expressed, these genes give ride to DNA-binding proteins
3. Bind to specific genes to regulate their expression
4. Ensuring correct gene expression to form specific anatomical structures.

Question 20

Explain how homeonoc genes control the body plan of an organism

Answer 20

1. Multiple homeobox genes in an organism’s genome.
2. During development, the embryo is divided into sections called somites.
3. Each somite expresses a different homeobox gene
4. Each homebox gene controls a different set if genes from the genome.
5. So each somite has a different gene expression pattern and develops different anatomical structures.
6. Hox genes also give rise to mitosis and apoptosis.

Question 21

Explain why mitosis and apoptosis are required during development.

Answer 21

1. As new anatomical structures are formed, more cells are required.
2. Increase in number of cells due to mitosis.
3. To shape structures properly, cell death is needed in a controlled way.
4. Cells undergoing apoptosis can release chemical signals to simulate mitosis and cell proliferation.
5. Hox genes regulate mitosis and apoptosis to control morphogenesis.