8.2: gene expression

stem cells are

unspecialised cells that can divide indefinitely and develop into other types of cell

stem cell become specialised during their development due to

different gene expresssion- only part of their DNA is transcribed and translated, they contain the same genes as specialised cells but they are not all expressed, different conditions means that different genes are expressed and switched off, genes that are expressed are transcribed to mRNA and translated into specific proteins, these proteins modify the cell and determine the cell structure and processes including the expression of more genes and the changes to the cell produced by these proteins causes the cell to become specialised

stem cells are classed by

their potentcy

potentcy is

the ability of a cell to differentiate into different cell types, the range depends on the source of stem cells

cells decrease in potentcy due to

epigenetic changes at each stage of development switching more and more genes off, reducing potency of cells, as cells differentiate the genes required remain switched on or become switched on

stem cells types classed in decreasing potency are

totipotent, pluripotent, multipotent, unipotent

totipotent cells are

able to differentiate into any type of cell found in the body and into extra embryonic cells such as those in the placenta

the source of totipotent cells is

in the embryo at an early stage called the blastomere, found in zygote and the cells before the blasocyst forms (early embryonic cells), for the first 5 days after fertilisation

pluripotent stem cells

can divide in unlimited numbers, they have the potential to develop into a limited number of cell types of a particular tissue or organ

source of pluripotent stem cells are

the inner mass of the blastocyst found in the embryo

multipotent stem cells

can differentiate into a limited number of cell types of a particular tissue or organ

source of multipotent stem cells are

body tissues of an adult or foetus like skin, muscle, brain, heart, bone marrow

unipotent stem cell

self renew by mitosis forming only one type of differentiated cell

source of unipotent stem cells are

in certain organs of mature mammals e.g cardiomyocytes on the heart

the way unipotent cell replace damaged cells is different from other differentiated cells as

they can divide by mitosis, regular differentiated cells die and are renewed by stem cell differentiation

totipotent stem cells are initially unspecialsed

however when they become specialised they differentiate to form tissues that make up the foetus, the cause of this is a change in gene expression where some genes are selectively switched on and off

uses of pluripotent cells are

they can be used to repair or replace damaged tissue because they can divide in unlimited numbers

ways to obtain stem cells are

spare embryos during IVF, cell removed from preimplantation genetic diagnosis at the 8 cell stage of an embryo, umbilical chord blood, mature mammals body tissue

stem cells can be removed from preimplantation genetic diagnosis at the 8 cell stage of an embryo

as the embryo can still develop normally and the cell can be cultured to produce stem cells

umbilical chord blood can be used to obtain stem cells as

it contains pluripotent cells that can be cultured

uses of stem cells are

medical therapies, drug testing, research

stem cells can be used to treat

leukaemia or replace abnormal blood, replace an entire tissue or organ injured or distressed, repair spinal chord injuries by replacing damaged neurones, treat diabetes by producing insulin-producing cells, repair damaged heart muscle cells after heart attack

sources of embryonic stem cells are

embryonic stem cells, therapeutic cloning to create embryonic stem cells, induced pluripotent stem cells, adult stem cells

embryonic stem cells are sources from

discarded IVF treatments, they are removed and cultures in a lab, which is given correct signals will differentiate into any cells type in the body, this can then be transplanted into patients

advantages of sources stem cells from embryonic stem cells are

pluripotent so develop into any cell type so can treat many diseases, embryos would’ve been discarded anyway, they can divide indefinitely and rapidly

disadvantages of using embryonic stem cells as a source are

limited number of embryos available and inconsistent supply as depends on consent and amount of treatments, risk of rejection since antigens on cell surface aren’t recognised by patients immune system so immunosuppressant drugs must be taken, ethical/religious concerns regarding destruction of something with potential for life, banned in some countries, small window to remove cells (day 5-14)

therapeutic cloning is a source of as

patients own body cells are used so embryonic stem cells produced aren’t reject as contain self antigens, its done by removing the nucleus from egg cell and removing the nucleus from a patients skin cell and inserting the nucleus into the egg cell, the cell is then shocked to encourage division, once blastocyst forms remove the embryonic stem cells and culture them in a lab

induced pluripotent stem cells are a source as

a small number of genes are only expressed in embryonic pluripotent stem cells and not in full differentiated cells, introducing these 4 genes back into the DNA of differentiated cells make them behave pluripotent, these genes code for transcription factors so inserting them back into the cells DNA, using viruses, switches on genes that had been switched off

summary of induced pluripotent stem cells is

from mature, fully specialised (somatic) cells, the cells regains capacity to differentiate through the use of proteins, in particular transcription factors

adult stem cells are a source as

they can be isolated from tissue where they reside and either be given signals in lab to differentiate which is then transplanted to patient, or transplanted to patient so they will then produce all the cells the stem cell differentiates to. because stem cells self-renew the patient will continuously be able to produce healthy cells

advantages of adult stem cells are

no ethical issues regarding gathering, usually no issues with immune rejection as long a donor is a clone tissue match e.g sibling

disadvantages of adult stem cells are

large number needed for most treatments and hard to find in large numbers, only differentiate to limited amount of cells since multipotent, difficult to identify and retrieve due to their location in the body, retrieval can be painful

summary of how cells become specialised is

genes are expressed, mRNA transcribed and translated into proteins, proteins modify the cell, cell becomes specialised for a particular function, genes switched off, mRNA will not be transcribed or translated

gene expression is regulated by

control factors that affect transcriptional factors, control factors post transcription

a transcription factor is

a protein that controls/regulates transcription of genes so that only certain parts of DNA are expressed

in eukaryotes, transcription factors work by

moving from the cytoplasm into the nucleus where they bind to promoter regions of DNA upstream (near the start) of target gene, the binding of the transcription factor makes it easier for RNA polymerase to bind, activates transcription

activator and repressor proteins

further control transcription by either increasing or decreasing the rate of transcription or prevent RNA polymerase from binding entirely

an example of a hormone effecting transcription is

oestrogen, a steroid hormone which binds to transcriptional factors called oestrogen receptors

steroid molecules are

small, hydrophobic, lipid based hormones that diffuse through membrane and go through nuclear pores

oestrogen plays a major role in

ovulation, implantation, maintaining pregnancy, childbirth and lactation

process of oestrogen effecting transcription is

oestrogen is lipid soluble so diffuses across the cell surface membran, it binds to an oestrogen receptor which acts as a transcriptional factor in the cytoplasm forming oestrogen-oestrogen receptor complex, which cause the er to change shape in its DNA binding site, e-er complex moves from cytoplasm and into nucleus through the nuclear pore where it binds to the promoter region of the gene stimulating binding of RNA polymerase

oestrogen can act as an activator or repressor as

it depends on the change in shape of the DNA binding site on the oestrogen receptor, if it makes it easier to bind then will increase, harder then will decrease

control factors post transcription are

RNAi, it occurs in eukaryotes and some prokaryotes

RNAi is

RNA interface, it enables a cell to prevent the expression of a gene even though the gene is switched on through either breaking down mRNA, or preventing ribosomes from translating mRNA

some scientists believe there is a selective advantage to having RNAi as

it has protection against viruses

RNAi is used for

the regulation of gene expression as not all genes should be expressed at all times, defence against viruses

RNAi can be a defence against viruses because

many viruses introduce double stranded RNA which cells recognise as abnormal so siRNA targets and degrades viral mRNA, preventing viral protein synthesis

proteins involved in RNAi are

dicer and risc

dicer is

a protein that cuts RNAi precursors to make them functional, it starts with a single stranded RNA that folds into a hairpin, or dsRNA and the dicer cuts near the loop to make a short RNA fragment for miRNA

risc is

RNA-induced silencing complex, the short siRNA/miRNA molecules formed by dicer bind to RISC, which helps them to their complementary mRNA molecules and bind to them, reducing gene expression

siRNA

causes complete degradation of mRNA, leading to gene silencing an is specific to one gene

siRNA is found in

the cytoplasm

siRNA works by

dsRNA is cut into siRNA by Dicer, one stand binds to RISC, siRNA is fully complementary to the target mRNA and will bind by complementary base pairs, mRNA is cleaved and degraded (cut into fragments)

miRNA

inhibits the translation or causes potential degradation of mRNA, reduces the rate of protein synthesis, can be useed for multiple genes

process of miRNA is

miRNA is a hairpin bend, it associates and is processed by Dicer, binds to RISC, it is partially complementary to mRNA so binds by complementary base pairing and physically blocks translation

miRNA is found

in the cytoplasm of all eukaryotic cells and is important for development and cell differentiation

miRNAs original structure is

a hairpin bend which is made from a single strand of RNA and parts of the strand are complementary to eachother so it folds back on itself, the step being paired bases and loop unpaired bases

the importance of the hairpin bend is

for recognition and processing, hairpin shape is recognised by enzymes, without the hairpin miRNA cannot be processed

real life applications of RNAi are

identifying the function of genes in cells or simple organisms, genetically modifying crops, treating human patients from diseases

RNAi can help identify the function of genes in cells or simple organisms

silencing the gene and observing the functional effects

RNAi can be used for genetically modifying crops as

it can silence undesirable genes e.g ones for toxins and allergens

RNAi can be used for treating human patients

to silence essential genes in cancer cells or auto viral therapies, e.g by silencing the genes for receptor protein used by HIV

RNAi can be used in plants to

provide resistance to viruses, pests and diseases, prevent spoilage by preventing bruising and browning, increasing nutritional value, reducing specific compounds such as caffeine in crops

the lac repressor transcriptional factor

controls the transcription of B galactosidase which digests lactose in E.coli, the enzyme is only transcribed in the presence of lactose so if no lactose, no enzyme made. if no lactose is present the lac repressor bind to DNA and blocks transcription but if lactose is present it binds to the lac repressor

epigenetics is

heritable changes in gene function without changing the base sequence of DNA

epigenetic changes alter

how easy it is for enzymes and other proteins needed for transcription to interact with DNA, by attachment or removal or epigenetic markers like methyl or acetyl groups

epigenetic changes have a role in

normal cellular processes and responses to changes in environment, they can be passed onto offspring

in order for a gene to be transcribed

appropriate transcriptional factor must be able to attach to promoter region of a gene and therefore DNA polymerase must be able to attach to the start of the gene

the attachment of transcriptional factors and RNA polymerase can be prevented epigenetically by

DNA remaining tightly coiled around the histone proteins within the chromosome, caused by acetyl groups, addition of methyl groups to some bases in the DNA prevent the attachment of transcriptional factors to promoter regions, as a result transcription of the gene is inhibited without altering the DNA sequence

DNA methylation is

the addition of methyl (CH3) groups to bases in the DNA molecule at CpG sites

methylation of DNA affects gene transcription because

it prevents the binding of transcriptional factors to the promoter region of the gene to be transcribed, inhibiting transcription as RNA polymerase won’t bind. methyl also attracts proteins that induce decreased acetylation

heterochromatin is

a tightly packed and transcriptionally inactive chromatin

euchromatin is

loosely packed and transcriptionally active

acetylation of histones

changes DNA structure, making histones either bind more or less tightly to DNA

acetylation works as

histones are positively charged proteins and DNA is a negatively charged molecule and is wrapped around the histone protein as opposite charges attract

DNA is negatively charged

due to presence of phosphate groups

in acetylation the acetyl group is added to

the histone tail, donated by acetyl coenzyme A, making the histone protein negatively charged/less positive

decreased acetylation causes transcription to be suppressed because

the additional of acetyl groups makes positively charged histones less positive/negative, if histones remain more positive, due to the absence of acetyl, they are more attracted to the negatively charged DNA since opposite charges attract. this means the DNA binds more tightly to the histone so transcriptional factors can no longer bind to promoter regions so the gene is switched off

epigenetic changes could affect humans

they can cause disease either by over activating a genes function or suppressing it

acetylation and methylation can be used as drug targets as

you can get DNA methylation inhibitors, or inhibitors for deacetylation (so encourage increased acetylation) to allow genes to switch on that have been switched off

acetylation used in drug targets as

histone deacetylation inhibitors are used in cancer therapy to switch on genes that have been switched off, they all the gene to be activated as the gene would remain acetylated so it can be transcribed since the chromatin would be less condensed and promoter accessible

DNA methylation can be used as drug target as

DNA methylation inhibitors can switch on genes that have been switched of, they can be used to treat various cancer and psychotic diseases such as schizophrenia

cancer can arise as

a result of mutation or epigenetic modifications and uncontrolled cell division in cancer leads to formation of a tumour

tumours can be

benign or malignant

benign tumours are

slow growing, non-cancerous and to not spread to other parts of the body, cells grow within a capsule and cannot invade neighbouring tissue and cause damage, they cells are fully differentiated like original cells and retain their normal function and shape

benign tumours cause harm

if they press against blood vessels or other cells causing mechanical damage

malignant tumours

are cancerous and grow rapidly and uncontrollably, they can spread to other parts of the body and neighbouring cells via metastasis causing damage and disrupting the running of important processes, cells are undifferentiated

characteristics of tumour cells are

nucleus larger or darker than normal/multiple nuclei, don’t produce proteins needed to function correctly, irregular shape, different antigens on surface, unresponsive to growth regulation processes, divide by mitosis more frequently than normal cells

cancer can be caused by

biomedical factors, lifestyle factors, environmental factors

biomedical factors that cause cancer are

genetic susceptibility, hormonal factors in females

lifestyle factors that can cause cancer are

smoking, alcohol consumption, physical inactivity and obesity, chronic infection, diet

environmental factors that cause cancer are

sunlight, radiation, pollution

gene mutations can lead to cancer when

DNA is altered by a mutation changing the base sequence of a protooncogene or a tumour suppressor gene

gene mutation in a tumour suppressor gene can lead to cancer because

a tumour suppressor gene which produces protein that inhibit division, if the mutation causes the amino acid sequence to be altered, it changes the structure of the protein and therefore it may no longer be able to inhibit division, causing uncontrolled, rapid cell division

gene mutation of a protooncogene can lead to cancer because

the protooncogene produces proteins that drive cell division, if the mutation leads to overexpression of the oncogene so its always active and transcribed then this can lead to uncontrolled and rapid cell division

a protooncogene

stimulates cells to divide by producing proteins that stimulate cell division, allow the checkpoints of the cell cycle to be passed

oncogene is

are formed from mutated protooncogenes and are permanently switched on resulting in cell division that in uncontrolled, it does this by permanently activating a cell surface receptor or coding for a growth factor

a tumour suppressor gene

controls cell division, causing the cell cycle to stop when damage is detected, they also play a role in the programming of apoptosis

abnormal methylation and acetylation can cause growth of tumours

as increased methylation (or decreased acetylation) of tumour suppressor genes or decreased methylation (or increased acetylation) of proto-oncogenes

increased methylation of tumour suppressor genes

known as hypermethylation, means transcription of tumour suppressor gene is inhibited, so the gene is switched off, therefore the protein that slows cell division and repairs DNA is not produced leading to uncontrolled cell division