Chapter 20: Gene expression Flashcards
Define a gene mutation
- changes or rearrangements to nucleotide bases in DNA molecule
- arise spontaneously during DNA replication i.e. interphase
mutation rate increased by…
- mutagenic agents:
high energy ionising radiation - alpha, beta particles and short wavelength radiation (e.g. x-rays and ultraviolet) disrupt DNA structure
chemicals - e.g. NO2 disrupts DNA structure or interferes w/ transcription e.g. inactivates tumour suppressor genes causing cancer
name all types of gene mutations
Substitution, Deletion, Addition, Duplication, Inversion and Translocation of bases
Define substitution mutation and list three possible outcomes it has on protein produced
- one base pair is replaced by a different base pair in DNA sequence
3 possible outcomes:
- forms stop codon: production of polypeptide chain stopped prematurely, protein won’t perform normal function
- formation of codon for different amino acid: polypeptide chain differs so protein produced has different structure and function; if enzyme no E-S complexes form as substrate no longer complementary to changed shape of AS
- produces codon for same amino acid: genetic code is degenerate i.e. amino acids have more than one codon, so mutation has no effect on polypeptide produced
define deletion mutation and explain the possible impact on phenotype
- loss of nucleotide base from DNA base sequence
- causes frameshift to left and bases read in wrong three base reading frame, codons and AA altered, so polypeptide structure will differ leading to different/non-functioning protein
- less impact on phenotype if deletion occurs near end of sequence as less bases affected
define addition mutation and explain the impact on phenotype
- extra base inserted in the DNA sequence
- frameshift to right and whole sequence altered (less impact at end of sequence), codons and AA altered so polypeptide structure differs leading to non/different functioning protein
when might an addition mutation have little effect on polypeptide?
- 3 bases or multiple of three bases are added
- bases are read in same reading frame so less impact on resulting polypeptide
define duplication mutation
one or more bases are repeated, produces frameshift to the right
- essentially a type of addition mutation
define ‘inversion of bases’ mutation and explain the impact
- group of bases separated from DNA sequence and rejoin at same position but in inverse order
- affects AA sequence produced and so polypeptide chain, this may change the structure of protein leading to possibly different or non-functioning protein
define ‘translocation of bases’ mutation and explain the possible impact on phenotype
- groups of bases become separated from DNA sequence on one chromosome and inserted into DNA sequence of another chromosome
- significant effects on gene expression leading to abnormal phenotype e.g. developing certain forms of cancer and infertility
mutations in body cells, rather than games lead to what?
disruption of normal cellular activity, like cell division e.g. cancer
what is cell potency?
- refers to varying ability of stem cells to differentiate into specialised cell types
- cells with greatest potency can generate more cell types than those with lower potency
what is cell differentiation?
process where undifferntiated/unspecialised cells develop into specialised structure suited for their function
explain how all cells contain all genes yet they carry out different functions and suggest why this is beneficial
- some genes are switched on and off (expressed or not)
- genes that are switched on, code for AA sequences of polypeptide, therefore gene is expressed (i.e. only part of DNA translated into proteins)
- different structures mean proteins carry out different specialised functions
(proteins usually produced include those involved in processes like respiration and membrane synthesis)
- beneficial: conserves energy and resources
name 2 methods involved in ensuring genes for proteins aren’t expressed:
a. preventing transcription and so preventing production of mRNA
b. preventing translation
Define stem cells and give examples
- undifferntiated cells that can divide and develop into specialised cells.
- Examples include totipotent, pluripotent, multipotent and unipotent cells
state 2 characteristics of stem cells
(1) Will replace themselves / keep dividing / replicate;
(2) Undifferentiated / can differentiate / develop into other cells / totipotent /
multipotent / pluripotent;
distinguish between totipotent, pluripotent, multipotent and unipotent cells
totipotent - can differentiate into any type of body cell and comprise first few cells that form zygote/early embryo
pluripotent - can differentiate into almost any type of cell (not placenta/extra-embryonic cells). Found in embryo and young fetus.
Multipotent - can differentiate into limited number of cells. Found in umbilical cord and some adult tissues e.g. bone marrow.
Unipotent - can only differentiate into a single type of cell and found in adult tissue e.g. cardiomyocytes = heart muscle cells divide to produce new heart tissue or repair damage to heart muscle
What happens to totipotent cells during embryonic development?
- Certain parts of the DNA are selectively translated so that only some genes are ‘switched on’, in order to differentiate the cell into a specific type and form the tissues that make up the foetus
Which types of stem cell are found in embryos?
Totipotent and pluripotent.
Multipotent and unipotent cells are only
found in mature mammals
where are totipotent stem cells found?
early embryonic tissues i.e. zygote (derive from first few cells after ferilisation)
what is totipotency?
any cell, such as a fertilised egg, which can mature into any body cell
where are pluripotent stem cells found?
embryo (but not extra embryonic cells i.e. placenta)
where are multipotent stem cells found?
adult tissue and in umbilical cord blood
where are unipotent stem cells found?
found in adults (such as bone marrow)
- usually done between family members b/c of tissue compatibility
what are induced pluripotent stem cells (iPS cells) ?
type of pluripotent cells produced from unipotent/somatic body cells
- genetically alerted to give characteristics of embryonic stem cell (type of pluripoent cell), involves inducing genes and Transcription factors (TFs)
how are iPS produced?
- somatic cell removed from individual
- manipulate DNA by injecting genes and TFs
- after repeated divisions, cells become pluripotent
benefits of iPS
- Used to produce transplant tissues or treat diseases but doesn’t destroy embryos ( ethical)
- iPS can be made using patient’s own cells ( less likely for rejection)
- Self-renewal - divide indefinetly and limitless supply for research
drawbacks of multipotent cells
- Found in small quantities
- Take time to mature
- Adult stem cell could be damaged and not used
- They are further along the specialisation pathway
name two current stem cell therapies
- bone marrow transplants
2. replace damaged tissues
Give a unique feature of pluripotent cells and the use of this feature.
- can divide in unlimited numbers,
and can therefore be used to repair or
replace damaged tissue.
(i.e. self-renewal)
What is a unipotent cell? Give an example
- cell that can only develop into one type
of cell - happens at the end of specialisation when the cell can only propagate its own type - example is cardiomyocytes (heart cells)
Give some uses of stem cells
- Medical therapies e.g. bone marrow
transplants, treating blood disorders. - Drug testing on artificially grown tissues.
- Research e.g. on formation of organs and embryos
Discuss the drawbacks/ethical issues in using stem cells in human disorders
- for theraputic cloning, is it right to create embryos for therapy and destroy them in the process?
- source of embryonic stem cells is unused embryos produced by IVF
- embryos could come to be viewed as a commodity rather than potential person
- at what stage of its development should embryo be treated as a person?
Discuss the drawbacks/ethical issues in using stem cells in treating human disorders
- for theraputic cloning, is it right to create embryos for therapy and destroy them in the process?
- source of embryonic stem cells is unused embryos produced by IVF
- embryos could come to be viewed as a commodity rather than potential person
- at what stage of its development should embryo be treated as a person?
Discuss benefits of using stem cells in treating human disorders
- a viable source of replacement cells to treat diseases and can potentially reduce morbidity and mortality for those waiting for transplants
- new drugs can be tested on stem cells rather than animals and humans
What molecules control the transcription of genes?
Transcription factors (TFs)
Where are promoter regions found?
Near the start of their target genes
What’s a transcription factor?
- protein that moves from cytoplasm to DNA
- binds to promoter region of DNA/gene and inhibits or promotes binding of RNA polymerase for transcription (i.e. controls gene expression)
How do transcription factors work?
- Move from the cytoplasm into nucleus.
- Bind to promoter region upstream of target gene.
- Makes it easier or more difficult for RNA polymerase to bind to gene. This increases or decreases rate of transcription.
Transcription of a gene can only occur when…what?
- when TF from cytoplasm enters nucleus and binds to its complementary DNA base sequences, initiating transcription of genes (i.e. allows RNA polymerase to bind) creating mRNA molecule
(w/o binding of TF gene is inactive and protein won’t be made)
Give an example of a hormone that affects transcription
oestrogen
binds to TF, which then initiates transcription of a gene
how is oestrogen able to diffuse through cell membrane?
it’s lipid-soluble
Describe the role of oestrogen in initiating transcription
- oestrogen diffuses through cell membrane.
- Forms oestrogen-receptor complex with ER 𝛼 receptor on TF in the cytoplasm (as its complementary), activating it
- activated oestrogen-ER alpha receptor complex (transcriptional factor) enters the nucleus and binds to the promoter region of the DNA, stimulates RNA polymerase to transcribe the gene
How can bone marrow transplant be used to treat diseases of the blood in two steps?
- Bone marrow transplants replaces the faulty bone marrow in patients with abnormal blood cells.
- The stem cells used divide and specialise to produce healthy blood cells.
What are the two types of transcription factors?
TF called ‘activators’ stimulate/increase rate of transcription by helping RNA polymerase bind to start of target gene and activate transcription
TF called ‘repressors’ inhibit/decrease rate of transcription by binding to start of target gene, preventing RNA polymerase from binding, preventing transcription
what is epigenetics?
A heritable change in gene function
without change to the base sequence of
DNA
what is the epigenome and its impact on gene expression
- epigenome = single layer of chemical tags on DNA
- impacts shape of DNA-histone complex, if DNA is tightly wound, unable to read so won’t be transcribed or expressed (epigenetic silencing)
OR
unwound so DNA is exposed and easily transcribed (switches them on)
epigenetics is caused by what changes?
- changes in environment e.g. diet, stress (can cause chemical tags to adjust wrapping or unwrapping of DNA and so switch genes on/off)
what’s a chromatin?
substance within a chromosome consisting of DNA and protein (usually histone)
How does increased methylation of DNA affect gene transcription?
- Involves addition of a CH3 group to
cytosine bases (which are next to guanine) - prevents transcription factors from binding.
- therefore gene transcription is
suppressed
why does increased methylation of DNA cause DNA to tightly coil around histones?
- methyl groups have positive charge, DNA has negative charge
- causes DNA and methyl groups to attract and tightly coil together
- so gene no accessible to TF to initiate transcription (i.e. gene turned off)
therefore increased methylation inhibits transcription
How does decreased acetylation of
histones affect gene transcription?
- acetyl groups bind to histones
- acetyl groups negatively charged like DNA and so they repel each other
- therefore DNA doesn’t tightly coil, it’s more loosely packed so DNA is more accessible for TF to bind
- therefore gene is transcribed and expressed
BUT when acetylation decreased (i.e. acetyl groups removed) from DNA, histones become more positive and so bind to DNA more tightly
therefore decreased acetylation inhibits transcription
what is heterochromatin?
genetically inactive part of genome, it has condensed chromatin structure and is inactive for transcription (tightly packed form of DNA -silent chromatin):
- increased methylation (of DNA inhibits transcription)
- decreased acetylation (of associated histones on DNA inhibits transcription)
what is euchromatin?
- loose chromatin structure and active for transcription (lightly packed form of chromatin):
- decreased methylation
- increased acetylation (off associated histone proteins)
What does epigenetics control?
gene expression in eurkaryotes
How might epigenetic changes affect
humans?
They can cause disease, either by over
activating a gene’s function (such as in
cancer) or by suppressing it.
How are epigenetic changes inherited?
Most tags removed between generations
Some passed on to offspring
When will methyl groups attach to cytosine?
When its next to guanine
How can epigenetic changes in tumor suppressor genes cause cancer?
genes hypermethylated
Genes not transcribed
Proteins not produced which slow cell division
Cells divide uncontrollably by mitosis- tumors
How can epigenetic changes in proto-oncogenes cause cancer?
Genes hypomethylated (i.e. not enough)
Act as oncogenes
Increasing production of proteins which encourage/initiate cell division
Cells divide uncontrollably by mitosis - tumour
What is the role of oestrogen in breast cancer?
Increased exposure to oestrogen for long time may increase risk of developing breast cancer
What are the theories linking oestrogen to breast cancer?
- Oestrogen stimulates certain breast cells to divide - higher chance of cells becoming cancerous
- If cells become cancerous, oestrogen stimulates further replication - tumours form quickly
- Oestrogen introduces mutations into DNA of certain breast cells
what is RNAi?
RNA interference
- inhibits translation of mRNA produced from target genes in eukaryotes and some prokaryotes
- done by destroying mRNA before its translated to create polypeptide chain
Oestrogen is a hormone that affects transcription. It forms a complex with a receptor in the cytoplasm of target cells. Explain how an activated oestrogen receptor affects the target cell. (2)
Stimulates RNA polymerase;
Increases transcription
oestrogen only affects target cells. Explain why oestrogen doesn’t not affect other cells in the body. (1 MARK)
- other cells don’t have oestrogen receptors
Give three possible uses of stem cells which have been grown in vitro and then induced to develop into a wide range of different human tissues. (3)
- Used to regrow tissues that have been damaged such as:
- heart muscle cells which have been damaged due to heart attack;
- skin cells which have been damaged by burns or wounds;
- can be used to produce B cells of the islets of Langerhans in people with Type I diabetes
Suggest one ethical argument for and one against stem cell research. (2)
For:
It is wrong to allow human suffering when there is a possibility of alleviating it by obtaining information from research;
Against:
Embryos should be given same respect as an adult person
Give two characteristic features of stem cells. (2)
Will replace themselves;
Undifferentiated
Explain what causes the siRNA to attach only to one sort of mRNA molecule. (1)
Has complementary base sequence
Describe and explain how expression of the target gene is affected by siRNA. (2)
No longer able to make specific protein;
Because mRNA has been cut into pieces
Scientists have suggested that siRNA may be useful in treating some diseases.
Suggest why siRNA may be useful in treating disease. (2)
Some diseases are genetic;
siRNA will stop product of this gene
Preventing the expression of a gene can be done by preventing transcription. Outline how this occurs. (2)
- Binding site on transcriptional factor that binds to DNA is blocked by an inhibitor molecule;
- Prevents transcriptional factor binding to DNA so prevents transcription and protein synthesis
Describe how oestrogen affects gene expression. (5)
1 Oestrogen combines with a complementary site on a receptor molecule of the transcriptional factor;
2 Oestrogen changes the shape of the receptor molecule;
3 Inhibitor molecule is released from DNA binding site;
4 Transcriptional factor can now bind with DNA;
5 Stimulates transcription of the gene and protein synthesis
Describe how siRNA affects gene expression. (5)
siRNA strand combines with an enzyme;
siRNA molecule guides enzyme to an mRNA molecule and pairs up its unpaired bases with mRNA’s complementary bases;
Enzyme cuts mRNA into smaller sections;
mRNA unable of being translated into a polypeptide
main characteristics of benign tumours
● Slow growth
● Defined by a clear boundary due to cell (so remain within tissue they arise)
adhesion molecules
● Cells retain function and normal shape
● Don’t spread easily/localised effect
● Easy to treat
● Nucleus has relatively normal appearance
main characteristics of malignant tumours
● Rapid, uncontrollable growth.
● Ill-defined boundary (finger-like
projections).
● Cells do not retain function and often die (become unspecialised)
● Spreads quickly and easily (metastasis).
● Difficult to treat
● nucleus often larger and appears darker due to abundance of DNA
Describe the role of tumour-suppressor genes
- Code for proteins that control cell division; in particular: slowing cell division preparing DNA mistakes programmed cell death (apoptosis)
Explain how tumour-suppressor genes can be involved in developing cancer
- mutation in the gene could code for a nonfunctional protein
- or increased methylation or
decreased acetylation could prevent transcription. - so cells will divide uncontrollably resulting in a tumour
Describe the role of proto-oncogenes
- code for proteins that stimulate cell division
- mutated form: oncogenes
Explain how proto-oncogenes can be
involved in developing cancer
- mutation in the gene could turn it into a permanently activated oncogene.
- decreased methylation or
increased acetylation can cause excess transcription - results in uncontrolled cell division and formation
of a tumour
Explain how abnormal methylation of genes can cause cancer
- hyper-methylation of tumour-suppressor genes or oncogenes can impair their function and cause the cell to divide uncontrollably
Explain how oestrogen can be involved in
developing breast cancer
- oestrogen is an activator of RNA polymerase
- therefore in areas of high oestrogen concentration, such as adipose tissue in the breasts, cell division can become uncontrolled
what is the genome?
- complete set of genetic information contained in the cells of an organism
What is genome sequencing?
- identifying the DNA base sequence of an individuals
- allows us to determine the amino acid sequence of the polypeptides coded for by that DNA
What is the proteome?
complete set of proteins that can be produced by a cell
can we directly translate the genome into the
proteome?
- in simple organisms, yes (e.g. prokaryotes)
- in complex organisms (e.g. euakaryotes), due to the presence of non-coding DNA (introns) and regulatory genes, it is much harder to obtain the proteome.
Give an application of sequencing the
proteome in simple organisms
- Identifying potential antigens for use in vaccine production
Give some applications of genome sequencing
● Comparing genomes between species to determine evolutionary relationships.
● Genetic matching.
● Personalised medicine.
● Synthetic biology (genetic engineering)
How have sequencing methods changed over time?
- used to be a manual process but
now it has become automated - reaction mixture is created and after the process is complete, a machine reads the base sequence
