Module 6: Section 1 - Cellular Control

Question 1

At what levels can gene expression be controlled?

Answer 1

Gene expression (and therefore protein synthesis) can be controlled at the transcriptional, post-transcriptional and post-transnational level. This happens via a number of different mechanisms.

Question 2

All the cells in an organisms carry the same genes (DNA) but the structure and function of different cells varies. Explain how.

Answer 2

All the cells in an organisms carry the same genes (DNA) but the structure and function of different cells varies. This is because not all the genes in a cell are expressed (transcribed and used to make a functional protein) - they are selectively switched on or off. Because cells show different gene expression, different proteins are made and these proteins modify the cell - they determine the cell structure and control cell processes (including the expression of more genes, which produce more proteins).

Question 3

Explain how transcription factors control gene expression at the transcriptional level

Answer 3

1) gene expression can be controlled at the transcriptional level by altering the rate of transcription of genes. e.g. increased transcription produces more mRNA, which can be used to make more protein
2) this is controlled by transcription factors - proteins that bind to DNA and switch genes on or off by increasing or decreasing the rate of transcription. Factors that increase the rate are called activators and those that decrease the rate are called repressors
3) the shape of a transcription factor determines whether it can bind to DNA or not, and can sometimes be altered by the binding of some molecules, e.g. certain hormones and sugars
4) this means the amount of certain molecules in an environment or a cell can control the synthesis of some proteins by affecting transcription factor binding
5) in eukaryotes, transcription factors bind to a specific DNA sites near the start of their target genes - the genes they control the expression of
6) in prokaryotes control of gene expression often involves transcription factors binding to operons

an operan is a section of DNA that contains a cluster of structural genes, that are transcribed together, as well as control elements and sometimes a regulatory gene:

Question 4

What is an operon?

Answer 4

An operan is a section of DNA that contains a cluster of structural genes, that are transcribed together, as well as control elements and sometimes a regulatory gene:

• the structural genes code for useful proteins, such as enzymes
• the control elements include a promoter (a DNA sequence located before the structural genes that RNA polymerase binds to) and an operator (a DNA sequence that transcription factors bind to)
• the regulatory gene codes for an activator or repressor

Question 5

Lac operon example:

1) E.coli is a bacterium that respires glucose, but it can use lactose if glucose isn’t available
2) the genes that produce the enzymes needed to respire lactose are found on an operon called the lac operon
3) the lac operon has three structural genes - lacZ, lacY and lacA, which produce proteins that help the bacteria digest lactose (including beta-galactosidase and lactose permease).

How does this work when lactose is present and when lactose is NOT present? See page 186 for diagrams

Answer 5

Lactose present:
When lactose is present, it binds to the repressor, changing the repressor’s shape so that it can no longer bind to the operator site. RNA polymerase can now begin transcription of the structural genes.

Lactose NOT present:
The regulatory gene (lacl) produces the lac repressor, which is a transcription factor that binds to the operator site when there’s no lactose present. This blocks transcription because RNA polymerase can’t bind to the promoter.

Question 6

Explain how mRNA is edited at a post-transcriptional level

Answer 6

1) genes in eukaryotic DNA contain sections that don’t code for amino acids
2) these sections of DNA are called introns. All the bits that do code for amino acids are called exons
3) during transcription the introns and exons are both copied into mRNA. mRNA strands containing introns and exons are called primary mRNA transcripts
4) introns are removed from primary mRNA strands by a process called splicing - introns are removed and exons joined, forming mature mRNA strands. This takes place in the nucleus
5) the mature mRNA then leaves the nucleus for the next stage of protein synthesis (translation)

Question 7

Explain how cyclic AMP (cAMP) activates some proteins at the post-transcriptional level and why this is necessary

Answer 7

1) some proteins aren’t functional straight after they have been synthesised - they need to be activated to work
2) protein activation is controlled by molecules, e.g. hormones and sugars
3) some of these molecules work by binding to cell membranes and triggering the production of cyclic AMP (cAMP) inside the cell
4) cAMP then activates proteins inside the cell by altering their 3D structure
5) for example, altering the 3D structure can change the active site of an enzyme, making it become more or less active

Question 8

Explain how cAMP activates protein kinase A (PKA)

Answer 8

1) PKA is an enzyme made of four subunits
2) when cAMP isn’t bound, the four units are bound together and are inactive
3) when cAMP binds, it causes a change in the enzyme’s 3D structure, releasing the active subunits - PKA is now active

Question 9

Please explain how Hox genes control development

Answer 9

1) homeobox sequences code for a part of the protein called the homeodomain
2) the homeodomain binds to specific sites on DNA, enabling the protein to work as a transcription factor
3) the proteins bind to DNA at the start of the developmental genes, activating or repressing transcription and so altering the production of proteins involved in the development of the body plan

Question 10

What is a body plan and what controls the development of a body plan?

Answer 10

1) a body plan is the general structure of an organism
2) proteins control the development of a body plan - they help to set up the basic body plan so that everything is in the right place, e.g. legs grow where they should

Question 11

What are hox genes and why have they changed very little during the evolution of different organisms that possess homeobox sequences?

Answer 11

1) the proteins that control body plan development are coded for by genes called Hox genes
2) similar Hox genes are found in animals, plants and fungi, which means that body plan development is controlled in a similar way in flies, mice, humans, etc. Hox genes have regions called homeobox sequences, which are highly conserved - this means that these sequences have changed very little during the evolution of different organisms that possess these homeobox sequences

Question 12

Some cells die and break down as a normal part of development. This is a highly controlled process called apoptosis, or programmed cell death. Once apoptoses has been triggered, what are the three steps that the cell is broken down in?

Answer 12

1) enzymes inside the cell break down important cell components such as proteins in the cytoplasm and DNA in the nucleus
2) as the cell’s contents are broken down it begins to shrink and breaks up into fragments 4
3) the cell fragments are engulfed by phagocytes and digested

Question 13

Mitosis and differentiation create the bulk of the body parts and then apoptoses refines the parts by removing the unwanted structures. Explain this in the example of tadpoles developing into frogs please

Answer 13

for example, as tadpoles develop into frogs, their tail cells are removed by apoptosis and when hands and feet first develop in humans the digits (fingers and toes) are connected - they’re only separated when cells in the connecting tissue undergo apoptosis

Question 14

During development, genes that control apoptosis and genes that control mitosis are switched on and off in appropriate cells - why is this?

Answer 14

during development, genes that control apoptosis and genes that control mitosis are switched on and off in appropriate cells. This means that some cells die, whilst some new cells are produced and the correct body plan develops

Question 15

The genes that regulate apoptosis and progression through the cell cycle can respond to both internal and external stimuli. Please explain how a gene regulating apoptosis would respond to both, using examples

Answer 15

1) an internal stimulus could be DNA damage. If DNA damage is detected during the cell cycle, this can result in the expression of genes which cause the cycle to be paused and can even trigger apoptosis
2) an external stimulus, such as stress caused by a lack of nutrient availability, could result in gene expression that prevents cells from undergoing mitosis. Gene expression which leads to apoptosis being triggered can also be caused by an external stimulus such as attack by a pathogen

Question 16

What are three types of mutation?

Answer 16

1) substitution - one or more bases are swapped for another
2) deletion - one or more bases are removed
3) insertion - one or more bases are added

Question 17

The order of DNA bases in a gene determines the order of amino acids in a protein - how does this alter the protein?

Answer 17

the order of DNA bases in a gene determines the order of amino acids in a protein. If a mutation occurs in a gene, the primary structure of the protein it codes for could be altered

this may change the final 3D shape of the protein so it doesn’t work properly

Question 18

Why might some mutations have a neutral effect on a protein’s function?

Answer 18

• the mutation changes a base in a triplet, but the amino acid that the triplet codes for doesn’t change. This happens because some amino acids are coded for by more than one triplet, e.g. both TAT and TAC code for tyrosine, so if TAT is changed to TAT the amino acid won’t change
• the mutation produces a triplet that codes for a different amino acids, but the amino acid is chemically similar to the original so it functions like the original amino acid
• the mutated triplet codes for an amino acid not involved with the protein’s function, e.g. one that’s located far away from an enzyme’s active site, so the protein works as it normally does

Question 19

Give an example of a mutation with a beneficial effect please

Answer 19

some bacterial enzymes break down certain antibiotics. Mutations in the genes that code for these enzymes could make them work on a wider range of antibiotics. This is beneficial to the bacteria because antibiotic resistance can help them to survive

Question 20

Give an example of a mutation with a harmful effect please

Answer 20

Cystic fibrosis can be caused by a deletion of three bases in the gene that codes for the CFTR (cystic fibrosis transmembrane conductance regulator) protein. The mutated CFTR protein folds incorrectly, so it’s broken down. This leads to excess mucus productuion, which affects the lungs of CF sufferers