Topic 8: Gene Expression

Question 1

What is a mutation?

Answer 1

Any change in the structure of quantity of DNA in an organism.

Question 2

What is a gene mutation?

Answer 2

Any change or rearrangement of the nucleotide base sequence. Usually arise during DNA replication

Question 3

What is a chromosome mutation?

Answer 3

A change in the chromosome number of a cell. Can arise spontaneously during meiosis

Question 4

Name the different types of gene mutation

Answer 4

• Substitution
• Deletion
• Addition
• Duplication
• Inversion
• Translocation

Question 5

What is a substitution mutation and its possible effects?

Answer 5

A nucleotide is replaced by one with a different base.

• Could form one of the 3 stop codons that mark the end of a polypeptide, so its production is stopped prematurely = non-functional protein.
• Could form a codon for a different amino acid, changing the shape of the protein = non-functional.
• Could form a different codon that codes for the same amino acid, as DNA is degenerate = no effect

Question 6

What is a deletion mutation and its possible effects?

Answer 6

The loss of a nucleotide base.

Causes frame-shift, so the entire gene of triplets is read differently, causing a different primary structure and a non-functional protein

Question 7

What is an addition mutation and its possible effects?

Answer 7

An extra base is inserted into the sequence, causing frame-shift, unless a multiple of 3 bases are added (still causing the production of a different polypeptide and non-functional protein though)

Question 8

What is a duplication mutation and its possible effects?

Answer 8

One or more bases is repeated, causing frame-shift = non-functional protein

Question 9

What is an inverse mutation and its possible effects?

Answer 9

A group of bases become separated from the DNA sequence and rejoin at the same position but in reverse order, causing a change in amino acid sequence and possibly a non-functional protein.

Question 10

What is a translocation mutation and its possible effects?

Answer 10

A group of bases become separated from the DNA sequence of 1 chromosome and get inserted into another chromosome.

Significant effect on gene expression = a change in phenotype, e.g some cancers and reduced fertility

Question 11

What are some causes of mutations?

Answer 11

Can arise spontaneously during DNA replication = permanent changes to DNA.

Basic mutation rate can be increased by external factors called mutagenic agents / mutagens, e.g:

• High energy ionising radiation, e.g alpha and beta particles or short wavelength radiation (UV, X-ray)
• Chemicals, e.g nitrogen dioxide can directly alter the structure of DNA or interfere with transcription

Question 12

What are the positives and negatives of mutations?

Answer 12

Produce the genetic diversity necessary for natural selection and speciation, but are almost always harmful, producing an organism less suited to its environment.

Also, mutations that occur in body cells not gametes lead to disruption of normal cellular activities, e.g cell division (leading to cancer)

Question 13

What is cell differentiation?

Answer 13

The process by which a cell develops into a specialised structure suited to the role it will carry out.

Question 14

Why does cell differentiation occur?

Answer 14

Because no one cell can provide the best conditions for all functions. All cells in an organism have the entire genome (as all come from the mitosis divisions of the zygote), so are capable of every function. They only become specialised because only certain genes are expressed in any one cell at any time.

Some genes are permanently expressed in all cells (e.g respiratory enzymes, proteins for transcription). Others are permanently not expressed (e.g insulin genes in intestinal cells). Others are switched on and off as they are needed.

Genes can be prevented from being expressed either by preventing transcription (so mRNA production) or translation.

Question 15

What are stem cells?

Answer 15

Undifferentiated cells that can differentiate into other specialised cells, and constantly divide to replicate themselves.

Question 16

What are the different types of stem cell?

Answer 16

• Totipotent
• Pluripotent
• Multipotent
• Unipotent

Question 17

What are totipotent stem cells with examples?

Answer 17

Can differentiate into any type of specialised cell from that organism, e.g meristem tissue, cells from the zygote (fertilised egg) to the morula (early cells)

Question 18

What are pluripotent stem cells with examples?

Answer 18

Can differentiate into almost any type of cell, e.g embryonic stem cells (from the blastocyst), fetal stem cells

Question 19

What are multipotent stem cells with examples?

Answer 19

Can differentiate into a limited number of , specialised cells, e.g stem cells in bone marrow produce different types of blood cells, adult and umbilical cord stem cells

Question 20

What are unipotent stem cells with examples?

Answer 20

Can only differentiate into one type of cell. Derived from multipotent stem cells and made in adult tissue, e.g cardiomyocytes can only produce new heart muscle tissue

Question 21

Give some sources of mammalian stem cells

Answer 21

• Embryonic stem cells
• Umbilical cord stem cells
• Placental stem cells
• Adult stem cells (specific to a tissue for maintenance + repair)

Question 22

What are induced Pluripotent Stem Cells (iPS cells)?

Answer 22

A type of pluripotent cell made by genetically altering unipotent cells gathered from a patient (e.g cardiomyocytes, skin, liver cells).

They acquire many of the characteristics of embryonic stem cells by inducing genes using transcription factors. However, they are different to embryonic stem cells as they are capable of self-renewal, so there is a potentially limitless supply .

They could replace embryonic stem cells in medical research / treatment as they overcome many of the ethical issues.

Question 23

What are some of the downsides of induced pluripotent stem cells (iPS cells)?

Answer 23

• They can be expensive
• There are accessibility issues
• Could lead to cancers
• Could cause side effects
• Risks for the procedures to obtain the adult somatic cells

Question 24

Give some examples of diseases that can be cured using iPS cells

Answer 24

• Skeletal muscles: muscular dystrophy
• Nerve cells: Parkinson’s, Alzheimer’s, MS
• Bone cells: osteoperosis
• Beta cells of pancreas: type I diabetes
• Blood cells: leukaemia
• Cartilage cells: osteoarthritis
• Skin cells: burns and wounds

Question 25

What are transcriptional factors?

Answer 25

Protein complexes with different subunits that diffuse from the cytoplasm to DNA in the nucleus through nuclear pores, in order to stimulate transcription. There are many transcriptional factors, each with a DNA binding site specific to a particular gene.

Question 26

How do transcriptional factors work?

Answer 26

When a protein is needed, the gene is stimulated by the specific transcriptional factor, which initiates protein synthesis by binding to DNA at the promoter sequence. stimulating RNA polymerase to bind and start transcription. When the gene is not being expressed, an inhibitor molecule blocks the DNA binding site on the transcriptional factor, preventing it from binding to DNA and starting transcription.

Question 27

How do hormones regulate transcription?

Answer 27

Oestrogen is a steroid hormone so is lipid-soluble. - Oestrogen diffuses through the phospholipid bilayer of the cell-surface membrane into the cytoplasm. - It combines with the complementary site on the receptor molecule of the transcriptional factor = hormone-receptor complex. - This changes the shape of the transcriptional factor, releasing the inhibitor molecule and exposing the DNA binding site. - The transcriptional factor diffuses into the nucleus via a nuclear pore and binds to the promoter region of its specific DNA sequence, attracting co-factors to bind to it. - This complex stimulates RNA polymerase to bind to the DNA and start transcription.

Question 28

How does RNA interference prevent gene expression?

Answer 28

Small molecules of double-stranded RNA called small interfering RNA (siRNA) prevent translation of the mRNA produced. Occurs in eukaryotes and some prokaryotes. - Double-stranded RNA (dsRNA) is produced by RNA dependent RNA polymerase. - Dicer enzymes hydrolyse dsRNA into siRNA - Another enzyme combines with siRNA, which guides it to an mRNA molecule. - The siRNA molecules binds to the mRNA using complementary base pairing. - The enzyme hydrolyses mRNA into many fragments, preventing translation. - The gene is not expressed.

Question 29

What is epigenetics?

Answer 29

Environmental factors can cause inheritable change in gene functions without changing the genome itself, e.g diet, stress, toxins

Question 30

What is the epigenome?

Answer 30

The chemical tags on DNA and histones, which determine the shape of the DNA-histone complex and so influence gene expression

Question 31

Can the epigenome change and why?

Answer 31

The DNA code is fixed, but the epigenome is flexible, as chemical tags respond to environmental changes, adjusting the wrapping and unwrapping of DNA and so switching genes on and off. The epigenome of a cell is the accumulation of all the signals it has received during its lifetime, so acts as a cellular memory.

Question 32

What are the 2 epigenetic processes that prevent gene expression?

Answer 32

- Decreased acetylation - Increased methylation

Question 33

How does decreased acetylation change gene expression?

Answer 33

- Acetyl groups are negatively charged, and bind to histones. - Deacetylation increases the positive charge on histones, and so increases attraction to the negative phosphate groups on DNA. - Stronger association between histones and DNA means the DNA-histone complex is more condensed, so DNA is not accessible to transcriptional factors, and the gene is not expressed.

Question 34

How does increased methylation change gene expression?

Answer 34

- Methyl groups are positive and bind to the cytosines of DNA. - Increased methylation attracts the negative phosphate groups of DNA, causing it to condense, preventing the binding of transcriptional factors to DNA, so the gene is not expressed. - Also attracts proteins that condense the DNA-histone complex by inducing deacetylation of the histones, making DNA inaccessible to transcriptional factors.

Question 35

What type of tumours are cancerous?

Answer 35

Malignant tumours are cancerous, benign tumours are not.

Question 36

Give some differences between benign and malignant tumours

Answer 36

- Benign grow slowly to a large size, but malignant grow rapidly to large sizes. - Benign cells are often specialised with a normal-looking nucleus, malignant cells are unspecialised with large and dark nuclei (abundance of DNA). - Benign produce adhesion molecules that make them stick together + remain in the tissue = primary tumours, malignant don't produce these so metastasise to other regions = secondary tumours. - Benign surrounded by a capsule of dense tissue so remain a compact structure, no capsule with malignant so can grow finger-like projections into surrounding tissue - Benign less likely to be life-threatening but can disrupt organ function, malignant more dangerous as normal tissue replaced by cancer. - Benign usually have localised effects on body, but malignant has systemic effects (whole body e.g weight loss, fatigue). - Benign usually just removed by surgery, malignant removal usually involves surgery, chemotherapy, radiotherapy. - Benign rarely reoccur after treatment, malignant reoccur more often.

Question 37

How can metastasis of malignant tumours occur?

Answer 37

Forms secondary tumours either by travelling through the body via blood vessels or lymph ducts.

Question 38

What are the 2 main genes that play a role in cancer?

Answer 38

- Oncogenes - Tumour suppressor genes

Question 39

What are proto-oncogenes?

Answer 39

Proto-oncogenes stimulate cells to divide when growth factors attach to a protein receptor on the cell-surface membrane.

Question 40

What are oncogenes?

Answer 40

Mutated proto-oncogenes that are permanently switched on.

Question 41

How can oncogenes lead to cancer?

Answer 41

They are proto-oncogenes that are mutated to be permanently switched on. This could be because the receptor protein is permanently activated, so cell division is switched on even in the absence of growth factors, or the oncogene may code for a growth factor which is then produced excessively, causing cells to divide rapidly and uncontrollably. Hypomethylation in oncogenes can also lead to their activation, causing uncontrolled cell division = cancer.

Question 42

How can tumour-suppressor genes lead to cancer?

Answer 42

Tumour suppressor genes slow down cell division, repair mistakes in DNA and cause apoptosis (cell death). If these are inactivated, they stop inhibiting cell division, leading to cancer. Hypermethylation in the promoter region of tumour suppressor genes inactivates them, so transcription of the promoter regions is inhibited, and the gene is silenced.

Question 43

How can oestrogen lead to breast cancer?

Answer 43

Post-menopause = increased risk of breast cancer due to an increased oestrogen concentration (more is produced by fat cells of the breasts). The tumour then further increases oestrogen concentration, = increased development of the tumour. White blood cells that are drawn to the tumour increase oestrogen production further. Oestrogen can cause tumours if the gene it is promoting transcription for is one that controls cell division and growth.

Question 44

What are genome projects and generally how do they work?

Answer 44

Projects to determine the entire DNA base sequence of an organism. Maps the DNA base sequences that make up the genes, then maps the genes onto individual chromosomes to find the entire genome. Sequencing has been made possible by bioinformatics, using computers to read, store and organise biological data at a faster rate. Utilises algorithms to analyse and interpret this data.

Question 45

How does DNA sequencing in genome projects work?

Answer 45

Uses the technique of whole-genome-shotgun (WGS) sequencing. Researchers cut DNA into small, easily sequenced sections and use computer algorithms to align overlapping segments to assemble the whole genome.

Question 46

Why is genome sequencing important?

Answer 46

Millions of base variations associated with disease have been discovered, medical screening improvements has increased early identification and intervention, and we have established evolutionary links between species.

Question 47

What is the proteome?

Answer 47

All the proteins produced by a given type of cell/organism at a given time under specified conditions

Question 48

How difficult is sequencing the proteome of simpler organisms and why?

Answer 48

Relatively easy because most prokaryotes have just 1 circular piece of DNA not associated with histones, and there are no introns like in eukaryotes.

Question 49

Why is knowing the proteome of prokaryotes important?

Answer 49

The antigens produced by pathogens can be used in vaccines, and genes from organisms that can withstand toxic/extreme environments can be used in biofuels or to clean pollutants.

Question 50

How difficult is sequencing the proteome of complex organisms and why?

Answer 50

Much harder to to translate knowledge of the genome to the proteome, because the genome contains introns as well as genes that have a role in regulating other genes. A problem with the human proteome project is deciding whose DNA is used for the mapping, as all individuals have different base sequences.