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the control of gene expression Flashcards

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1
Q

what is a mutation?

A

change in the base sequence of DNA that often arises spontaneously during replication

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2
Q

types of mutation

A

addition, deletion, substitution, inversion, duplication and translocation

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3
Q

addition mutation

A

base added to sequence causing frame shift

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4
Q

deletion mutation

A

base removed causing frame shift

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5
Q

substitution mutation

A

one base changed for a different base (silent, nonsense or missense)

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6
Q

inversion mutation

A

section of bases detaches from the DNA sequence and rejoins inverted

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7
Q

duplication mutation

A

a whole gene or a section of a gene is duplicated so two copies appear on the same chromosome (mutation is not harmful but second copy can mutate)

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8
Q

translocation mutation

A

series of bases on one chromosome detaches and attaches onto a different chromosome

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9
Q

mutagenic agent

A

factors that increase the rate of gene mutation e.g high energy and ionising radiation and carcinogens

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10
Q

stem cell definition

A

undiffrentiated cells that can continually divide and become specialised

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11
Q

types of stem cells

A

totipotent, pluripotent, multipotent and unipotent

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12
Q

totipotent stem cells

A
  • stem cells that can divide and produce any type of body cell
  • occur for a limited time in early mammilian embryos (e.g zygote)
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13
Q

pluripotent stem cells

A
  • stem cells that are found in embryos and produce almost any type of cell apart from placenta and embryo
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14
Q

multipotent stem cells

A
  • diffrentiate into a limited number of cells (e.g blood cells)
  • found in bone marrow
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15
Q

unipotent stem cells

A
  • can only diffrentiate into only one type of cell
  • e.g epidermal stem cell or cadiomycocytes
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16
Q

induced pluripotent stem cells (iPS)

A

stem cells produced from adult somatic cells using transcription to help overcome some issues of embryonic stem cells

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17
Q

iPS process

A
  • created from adult unipotent cells and are altered to return them to a state of pluripotency
  • to do this, genes that were switched off to make the cell specialised must be switched back on
  • this is done using transcription factors
  • the iPS are very similar to embryonic pluripotent stem cells
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18
Q

unique feature of iPS

A

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

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19
Q

what is a transcriptor factor?

A

a protein that controls the transcription by binding to complementary promoter so that only certain parts of the DNA are expressed using DNA polymerase

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20
Q

how do transcription factors work?

A
  • move to cytoplasm into nucleus
  • bind to promoter region upstream of target gene
  • makes it easier/more difficult for RNA polymerase to bind to gene
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21
Q

how does oestrogen affect transcription?

A
  • oestrogen is lipid soluble so it can diffuse through the cell-surface membrane
  • oestrogen binds to a specific shaped transcription factor
  • oestrogen causes the transcription factor to change shape
  • the DNA binding site of the transcription factor is now complementary to the shape of the promoter region of the target gene
  • transcription factor complex diffuses into the nucleus through a nuclear pore
  • the transcription factor binds to promoter region of a gene and stimulates transcription
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22
Q

what is RNA interference (RNAi)?

A

when the translation of mRNA is prevented

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23
Q

what organisms does RNAi occur in?

A

eukaryotes and some prokaryotes

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24
Q

what RNA inhibits translation?

A

siRNA

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25
Q

process of RNAi

A
  • siRNA complementary to mRNA
  • siRNA bind to mRNA
  • ribosomes cannot bind to mRNA as it is double stranded
  • prevents translation of mRNA
  • no protein formed
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26
Q

what is cancer the result of?

A

mutations in genes that regulate mitosis, resulting in the uncontrollable divisions of cells and the creation of a tumour

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27
Q

characteristics of benign tumour

A
  • non cancerous
  • slow growth
  • defined by clear boundary due to adhesion molecules
  • impact is localised so does not spread
  • easy to treat
  • cells retain function and normal shape
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28
Q

characteristics of malignant tumours

A
  • cancerous
  • rapid, uncontrollable growth
  • difficult to treat
  • metastitise
  • do not produce adhesion
  • cell becomes unspecialised
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29
Q

how does chemotherapy work?

A
  • prevents DNA replication in interphase
  • prevents the formation of spindle fibres in prophase
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30
Q

what genes control cell division?

A

tumour-suppressor genes and proto-oncogenes

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31
Q

role of tumour-suppressor genes

A

code for proteins that control cell division when damage is detected (e.g DNA copying errors). help programme apoptosis. (stop cell division)

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31
Q

how can proto-oncogenes be involved in developing cancer?

A

mutation causes oncogenes to permanetly actiavte cell division

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31
Q

how can tumour-suppressor genes be involved in developing cancer?

A

hypomethylation/mutation results in coding a non-functional protein which does not inhibit cell division so mutations are not destroyed

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31
Q

role of proto-oncogenes

A

create proteins involved in the initiation of DNA replication and mitosis cell division when the body needs new cells (stimulate cell division)

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32
Q

how is abnormal methylation associted with cancer?

A

hypermethylation of tumour-suppressor genes (switched off) and hypomethylation of oncogenes (switched on)

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32
Q

what is meant by epigenetics?

A

a heritable change in gene function without change to the base sequence of DNA

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33
Q

how can increased oestrogen concentration be related to cancer?

A
  • oestrogen activates transcription factors to bind to activate RNA polymerase
  • cell division can therefore become uncontrolled
  • tumours results in even more oestrogen being produced
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34
Q

what factors can leave epigentic tags?

A

diet, stress and toxins

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35
Q

effect of DNA methylation

A
  • methylation of cytosine so promoter region methylates (+ve)
  • transcription factor cannot bind
  • because DNA-histone complex (-ve) is so tightly coiled because of attraction
  • transcription inhibited
  • uncontrolled cell division
36
Q

effect of DNA acetylation

A
  • acetylation (-ve) of histones cause DNA (-ve) to be repelled
  • causes DNA to be less tightly bound to histones
  • makes it easier for transcription factors to bind
  • increases transcription
37
Q

does an increase or decrease of methylation inhibit transcription?

A

increase

38
Q

does an increase or decrease of acetylation inhibit transcription?

A

decrease

39
Q

what is heterochromatin?

A

tightly coiled DNA caused by increased methylation and decreased acetylation

40
Q

what is the genome?

A

entire genetic material of an organism in a cell

41
Q

what is genome sequencing?

A

identifying the DNA base sequence for all DNA in a cell, this allows us to identify the amino acid sequence of the polypetides coded for by that DNA

42
Q

what is the proteome?

A

complete set of proteins that can be produced by a cell

43
Q

can we directly translate the genome into the proteome?

A

only in simple organisms like prokaryotes because they do not contain introns or regulatory genes

44
Q

application of proteome sequencing

A

identifying potential antigens to use in a vaccine

45
Q

applications of genome sequencing

A
  • comparing genomes to work out evolutionary relationships
  • personalised medicine
  • genetic matching
  • synthetic biology
46
Q

how have sequecning methods changed over time?

A

used to be a manual process however it is now automated as a machine reads the base sequence

47
Q

what is recombinant DNA technology?

A

the transfer of DNA fragments from one organism to another

48
Q

why does recombinant DNA technology work?

A

because the genetic code is universal and therefore transcription and translation occur by the same mechanism and result in the same amino acid sequence across organisms

49
Q

what three methods are used to create DNA fragments?

A

reverse transcriptase, restriction endonucleases and the gene machine

50
Q

reverse transcriptase process

A
  • RT makes DNA copies from mRNA
  • pure mRNA is isolated from target cell
  • RT joins free DNA nucleotides with comp bases to mRNA sequence
  • creates cDNA
  • DNA polymerase is used to make this double stranded
51
Q

advantage of cDNA

A

it is intron free because it is from the mRNA sequence, prokaryotes cannot remove introns

52
Q

restriction endonuclease process

A
  • hydrolyse DNA at specific recognition sites
  • cuts staggered ends to expose DNA bases
  • sticky ends are palindromic so can join by comp base pairing easily
53
Q

gene machine process

A
  • DNA fragments created in lab using gene machine
  • DNA sequence of protein is entered to computer
  • creates oligonucleotides
  • oligonucleotides join together to create single strand of DNA
54
Q

what is an oligonucleotide?

A

short overlapping single strands of nucleotide

55
Q

advantage and disadvantage of RT

A
  • lots of mRNA to make cDNA
  • more steps so more difficult
56
Q

advantage and disadvantage of RE

A
  • sticky ends makes it easier to insert DNA fragment
  • still contains introns
57
Q

advantage and disadvantage of gene machine

A
  • can design exact DNA fragment with sticky ends, labels and prefernetial codons
  • needs to know amino acid sequence
58
Q

two ways in which DNA can be amplified

A

in vitro- polymerase chain reaction
in vivo- using host cells

59
Q

stages of in vivo gene cloning

A
  1. creating DNA fragments
  2. inserting DNA fragments into a vector
  3. transformation of host cell
  4. identifying transformed clones
  5. growing the host cell
60
Q

inserting DNA fragment process

A
  • RE are used to cut out gene to make DNA fragments
  • promoter and terminator region are added
  • same RE is used to cut the DNA of a plasmid
  • this creates complementary sticky ends 0f the DNA fragments and the plasmid
  • pair are joined by ligase
  • ligase catalyses the condensation reaction to form PPD bonds between nucleotides
61
Q

transformation of host cell process

A
  • cell membrane of host cell is made more permeable
  • mixed with calcium ions and then heat shocked
  • enables vector to enter host cells cytoplasm
62
Q

what issues can arise with host cells taking up recombinant plasmid?

A
  • recombinant plasmid does not get inside the cell
  • plasmid rejoins before DNA fragment has entered
  • DNA fragment sticks to itself
63
Q

ways of identifying transformed cells

A
  • antibiotic resistance genes
  • fluorescent proteins genes
  • enzyme coding genes
64
Q

antiobiotic resistance process

A
  • insert gene for antibiotic resistance 1 and 2 into plasmid
  • insert DNA fragment into plasmid in the middle of antibiotic 1 gene
  • grow bacteria on agar
  • transfer bacteria colonies to a plate with antibiotic 2
  • any colonies that grow have the plasmid
  • transfer to a plate with antibiotic 1
  • colonies that don’t grow contain the DNA fragment
65
Q

fluorescent marker process

A
  • insert DNA fragment into middle of fluorescent protein gene in plasmid
  • use UV light
  • any non-glowing colonies contain recombinant plasmid
66
Q

enzyme markers process

A
  • plasmid with lactase enzyme has DNA fragment inserted into middle
  • prevents production of lactase
  • colonies which cannot turn the colourless substance blue contain the recombinant plasmid
67
Q

how to grow host cell for in vivo gene cloning?

A

use a fermenter which grows multiple copies of the host cell

68
Q

what is used for in vitro cloning?

A

PCR

69
Q

equipment and their uses for PCR

A
  • thermocycler (temp change)
  • DNA fragments
  • DNA polymerase (Taq polymerase which makes new polymer chains of DNA)
  • primers (complementary to start and end of DNA fragment)
  • DNA nucleotides
70
Q

what is a primer?

A

short sequence of single stranded DNA that are complementary to the start and end of a DNA fragment

71
Q

PCR process

A
  • separation: temp increases to 95c to break H+ bonds and split DNA fragment into single strands
  • annealing of primers: temperature decreased to 55c so that primers can attach and form H+ bonds
  • extension: DNA polymerase binds to primer and attaches comp free nucleotides and makes a new strand to align next to template, temp increased to 72c
72
Q

advantages of PCR

A
  • automated so more efficient
  • rapid (100 billion copies of DNA can be made in hours)
  • does not require living cells
73
Q

what are VNTRs?

A

variable number tandem repeats in human DNA introns

74
Q

why are VNTRs compared?

A

the probability of two individuals having the same VNTRs is very low however the more closely related you are, the more similiar the VNTR

75
Q

what is genetic fingerprinting?

A

analysis of VNTR DNA fragments to determine genetic relationships and genetic variability

76
Q

steps of genetic fingerprinting

A
  1. collection
  2. extraction
  3. digestion
  4. separation
  5. hybridisation
  6. development
  7. analysis
77
Q

collection and extraction in genetic fingerprinting

A
  • small sample of DNA can be collected for genetic fingerprinting
  • e.g blood, body cells and hair follicles
  • small samples can be identified using PCR
78
Q

digestion in genetic fingerprinting

A

restriction endonucleases are used to cut VNTRs out

79
Q

separation in genetic fingerprinting

A
  • DNA samples loaded with small wells in agar gel
  • gel is placed in a buffer liquid with electrical voltage applied
  • DNA has -ve charge so move through towards other end of the gel (gel electrophoresis)
  • agar gel creates resistance so short fragments move faster and further
  • alkanine added
  • creates patterns of bands
80
Q

hybridisation in genetic fingerprinting

A
  • DNA probes are complementary in base sequence to VNTRs
  • the probes are radioactively or fluorescently labelled
  • probes mixed with VNTR
81
Q

development in genetic fingerprinting

A
  • DNA probes and VNTRs are transferred to a nylon sheet
  • can be exposed to x-ray or UV lights
82
Q

analysis in genetic fingerprinting

A
  • position of DNA bands are compared with known VNTR lengths to identify genetic relationships
83
Q

applications of genetic fingerprinting

A
  • paternity test
  • forensic science
  • ensure animals are not closely related before breeding
  • medical diagnosis
84
Q

how can genetic fingerprinting be used to measure paternity?

A

compare the bands of VNTRs in the mother, child and potential fathers. all of the child’s VNTRs must have been inherited from either the mother or father.

85
Q

what is a DNA probe?

A

short, single stranded pieces of DNA that can be labelled to locate specific alleles of genes

86
Q

how can DNA probes be used to locate specific alleles?

A

created to have a complementary base sequence to the allele being screened for. they are labelled, amplified using PCR and added to a sample of single stranded DNA, binding if the allele is present

87
Q

process of genetic screening

A
  • DNA probe made
  • fragment of DNA made using PCR
  • label is then added
  • after hybridisation the DNA is washed so any unbound DNA probes are removed
  • presence of label indicated allele of interest is present
88
Q

process of DNA hybridisation

A
  • DNA sample is heated to make it single stranded
  • single stranded DNA sample is mixed with DNA probe and cooled
89
Q

what can genetic screening be used for?

A
  • can identify heritable dieases early
  • personalised treatment
90
Q

personalised medicine application

A

some drugs such as painkillers are more or less effective depending on your genotype. it can aslo be used to identify the best dose, increasing effectiveness, safety and can save money.

91
Q

genetic counselling

A

type of social work where people can have their family history researched to consider the likelihood of them carrying any alleles linked to diseases before starting a family

biology (21 decks)

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