Gene expression is controlled by a number of features + Human Genome Project

stem cells

unspecialised cells capable of:

• self-renewal'; can divide to replace themselves

• specialisation/differentiation; can develop into other types of cell

stem cell specialisation

• stimulus e.g. chemical

• causes selective activation of genes - some genes activated while others inactivated, e.g. muscle cells genes coding for actin and myosin need to be activated

• mRNA only transcribed from active genes → translated on ribosomes = proteins

• these proteins modify cell permanently and determine cell structure/function

potency - types of stem cells

• totipotent cells

  • occur for a limited time in early mammalian embryos

  • can divide and differentiate into every cell type in body (including the cells that support the embryo, such as the placenta)

• pluripotent cells

  • found in embryos

  • can divide and differentiate into most cell types (every cell type in body but not the cells of the placenta)

• multipotent cells

  • found in mature mammals

  • can divide and differentiate into a limited number of cell types

  • e.g. multipotent cells in bone marrow can differentiate into different types of blood cell

• unipotent cells

  • found in mature mammals

  • can divide and differentiate into just one cell type

  • e.g. cardiomyocytes (cardiac muscle cells) can be made from unipotent stem cells

stem cells in medicine

• regrow damaged tissues in accidents (i.e. skin grafts) or by disease (i.e. neuro-degenerative diseases, Parkinson’s disease)

• lots of potential links to topic 6 e.g. B cells of the pancreas in type 1 diabetes

• drug testing - used to grow artificial tissues

• developmental biology research - provide insight into embryological development

Induced pluripotent stem cells

How they are produced:

1. produced from adult somatic cells (non-pluripotent cells or fibroblasts)

2. specific protein transcription factors associated with pluripotency put into cells, causing the cell to express genes associated with pluripotency (reprogrammed)

3. cells cultured

4. = induced pluripotent stem cells

Used in medical treatment instead of embryonic cells

• no immune rejection as can be made using patient’s own cells

• overcome some ethical issues with using embryonic stem cells e.g. no destruction of embryo and adult can give permission

Evaluate use of stem cells in treating human disorders

For:

• embryos are tiny balls of cells, incapable of feeling pain, not equivalent to human

• would otherwise be destroyed (if from infertility treatment which creates more than needed)

• duty to apply knowledge to relieve human suffering

Against:

• embryo is a potential human - should be given rights

• induced pluripotent stem cells - cannot yet reliably programme stem cells

• could begin to multiply out of control, and cause tumours

Regulation of transcription and translation

• transcription factors are proteins

• move from the cytoplasm → nucleus

• bind to DNA at a specific DNA base sequence on a promotor region (near start/upstream of target gene)

• stimulate (‘activator’) or inhibit (‘repressor’) transcription (the production of mRNA) of target gene(s) (by helping or preventing RNA polymerase binding)

The role of oestrogen in initiating transcription

1. oestrogen, a steroid hormone, can diffuse across the phospholipid bilayer of the cell-surface membrane as its lipid soluble

2. in the cytoplasm, oestrogen binds to a receptor of an inactive transcription factor, forming a hormone-receptor complex

3. inactive transcription factor changes shape, resulting in active transcription factor

4. diffuses from cytoplasm into nucleus and binds to specific DNA base sequence on a promotor region

5. stimulates transcription of genes by helping RNA polymerase to bind

Regulation at the chromosomal level : epigenetics

Nucleosome - DNA wrapped around histone proteins

• How closely the DNA and histone are packed together affects transcription

Epigenetics - heritable changes in gene function (expression) without changes to the base sequence of DNA, caused by the changes in the environment

• epigenetic changes can inhibit transcription:

  1. Methylation of DNA

  • Methyl groups added to cytosine bases in DNA

  • nucleosomes pack more tightly together → prevents transcription factors binding; genes not transcribed (RNA polymerase can’t bind)

  • irreversible

  2. Decreased acetylation of associated histones:

     • decreased acetylation of increases positive charge of histones

     • histones bind DNA (which is negatively charged) more tightly → preventing transcription factors binding; genes not transcribed

     • reversible

Relevance of epigenetics on disease development and treatment, especially cancer

• epigenetic changes that increase the expression of an oncogene, or that silence a tumour suppressor, can lead to tumour development (see next section)

• tests can be used to see if a patient has abnormal levels of methyl and acetyl - early indication of cancer (called biomarker)

• could be manipulated to treat cancer i.e. drugs to prevent histone acetylation/DNA methylation that may have caused these genes to be switched on/off, resulting in cancer

Regulation of translation: RNA interference (RNAi)

RNA interference (RNAi) - RNA molecules inhibit translation of mRNA produced by transcription (gene is ‘switched on’ but encoded protein not produced = ‘silenced’ gene)

• RNAi can be moderated by either siRNA or miRNA

  1. micro-RNA (miRNA)

     • formed as hair-pin bends of RNA but processed int single strands 22-26 nucleotides long, both become incorporated into a protein-based RISC (RNA induced silencing complex)

  2. Small interfering RNA (siRNA)

     • formed as a double-stranded molecules 21-25 bp long, one strand incorporated into a protein-based RISC

• Single-stranded miRNA/siRNA within a RISC binds to a molecule of mRNA containing a sequence of bases complementary to its own → mRNA hydrolysed/translation stopped

• miRNA expression deregulated in many human diseases including cancer → offer opportunities as biomarkers and novel therapies

Cancer

• uncontrolled cell division → tumour

• not all tumours are cancerous, they can be classified as:

  • Benign (non-cancerous; don’t spread) or

  • Malignant (cancerous; spread easily throughout the body via metastasis

Main characteristics of benign and malignant tumours

• B - grow slowly, M - grow rapidly

• B - well differentiated/specialised (cells retain function), M - cells become unspecialised/poorly differentiated

• B - normal, regular nuclei, M - irregular, larger/darker nuclei

• B - well defined borders/boundary; cell adhesion molecules stick cells together and to a particular tissue, often surrounded by a capsule so remain within tissues, M - Irregular/poorly defined borders and not encapsulated; cells break off (+grows projections into surrounding tissues) so metastasis occurs

• B - easy to treat; can normally be removed by surgery, rarely returns, M - removed by radiotherapy/chemotherapy as well as surgery; can be life threatening and recurrence more likely

The role of tumour suppressor genes and oncogenes in the development of tumours including their abnormal methylation

Tumour suppressor genes:

• normal function

  • code for proteins involved in control of cell division

  • especially in stopping cell cycle (when DNA damage detected)

  • also involved in causing self-destruction of cell (apoptosis) (where damaged DNA cannot be repaired)

• Role in the development of tumours

  • mutation alters amino acid sequence and tertiary structure of protein = non-functional protein

  • or increased methylation prevents transcription/expression of protein

  • damaged DNA not repaired/cells not killed; uncontrolled cell division

  • note - would need 2 mutated alleles

(proto)- oncogenes:

• normal function

  • code for proteins involved in control of cell division

  • especially in stimulating cell division (when growth factors attach to receptors on cell membrane, so cell division is required)

• Role in development of tumours

  • mutation could turn into permanently activated oncogene

  • decreased methylation/increased acetylation causes excess transcription

  • cell division permanently activated; rapid/uncontrolled cell division

  • note - only need 1 mutated allele

The role of increased oestrogen concentrations in the development of some breast cancers

• Areas of high oestrogen conc. such as adipose tissues in breasts, cell division uncontrolled

• growth of cancer minimised with drugs blocking production/action of oestrogens in the breasts e.g. Tamoxifen prevents oestrogen binding to the receptor

DNA sequencing

• Sequencing projects have read the genomes of a range of organisms (e.g. The Human Genome Project)

• Sequencing methods are continuously updated and have become automated

  • Past - labour-intensive, expensive, could only be done on a small scale

  • Now - automated, cost-effective and done on a large scale e.g. pyrosequencing

Applications of sequencing projects

Simple organisms:

• Determining the genome of simpler organisms allows the assignment of proteins to each gene in the genome (proteome), creating a database

• Easy because less non-coding DNA

• identifying the protein antigens on the surface of viruses/pathogenic bacteria can help in the development of vaccines

Complex organisms e.g. humans:

• knowledge of the genome cannot easily be translated into the proteome, due to the presence of:

  • Non-coding DNA

  • Regulatory genes - determine when the genes that code for particular proteins should be switched on and off

• Human Genome Project - determined the sequence of bases of a human gene