topic 8

Question 1

what is a base substitution and its consequences?

Answer 1

when one nucleotide is substituted
its effects are :
that codon could now code for a stop codon. breaking the polypeptide chain to early. this leads to a malfunctional protein
the codon could now code code for a different amino acid. changing the structure of the polypeptide chain being different. If its an enzyme it could be no longer complementary to the substrate
produces the same codon as DNA is degenerate

Question 2

what is the effect of base deletion?

Answer 2

causes a frame shift to cover the deletion.
this means every codon after will be altered
causes unfunctional polypeptides
will not be as harmful if its at the end

Question 3

what is the effect of addition of a base?

Answer 3

causes a frame shift to the left
polypeptide will be most likely unfunctional
if exactly 3 is added no shift as it is a new codon

Question 4

what is translocation,inversion and duplication of bases?

Answer 4

duplication- causes frame shift to the right
inversion-group of bases become seperated and rejoin back to front
translocation- group of bases become seperated from one chromosome and
rejoin at another chromosome has significant effects on gene
expression and hence phenotype

Question 5

what are the causes for mutations and its advandategs/disadvadvantages?

Answer 5

mutagenic agents which include
high energy ionising radiation-
chemicals such as nitrogen dioxide
its advantage is that it provides the genetic diversity needed for natural selection
its disadvantage is that it is nearly always harmful and produces an organism that is less suited to the environment

Question 6

what is cell differentiation?

Answer 6

in multicellular organisms every cell cannot complete all the tasks like single cell organims.This means cells must differentiate.they do this by turning on and off genes

Question 7

what is totipotency?

Answer 7

cells such as fertilised eggs which can mature into any body cell are known as totipotent cells. once matured they turn into specialised cells.

Question 8

how do specialised cells stop making irrelevant proteins?

Answer 8

specialised cells can still do all the functions however it would be a waste of energy. To stop this they prevent transcription and translation

Question 9

what are stem cells?

Answer 9

mature cells that can differentiate into other cells

Question 10

how do stem cells originate

Answer 10

embryos in the early stage of development
umbilical cord blood
placenta
adult stem cells (found in the body tissue)

Question 11

what are the types of stem cells

Answer 11

totipotent stem cells found in the early embryo and can differentiate into any type of cell
pluripotent stem cells- found in the embryo and can differentiate into almost any cell
multi potent stem cells - found in adult bone marrow and can differentiate into limited amount of cells
unipotent stem cell - found in adult can only differentiate into 1 cell

Question 12

what are induced pluripotent stem cells?

Answer 12

they are deduced from uni potent stem cells. it can be any body cell. these body cellls are then genetically altered to give them characteristic of pluripotent stem cell (embryo) by turning on genes that were off. they are capable of self renewal (self divide). They could become a good alternative for embryonic stem cells and overcome many of the ethical issues surrounding embryonic stem cells

Question 13

how is gene expression controlled by transcription?#

Answer 13

for transcription to begin the gene is switched on by (transcriptional factors)molecules that move from the cytoplasm into the nucleus
each transcriptional factor binds to a specific base in the DNA
this causes that reigon to begin transcription
mRNA is produced and the polypeptides are translated
when a gene is not being expressed the transcriptional factor site is inactive
this means that that section cannot be transcripted

Question 14

how do hormones such as oestrogen turn on DNA transcrption

Answer 14

oestrogen is lipid solouble so dissolves through phospholipid layer membrane
once inside oestrogen binds with site on receptor molecule of transcriptional factor
this changes the active site of transcriptional factor which is now acticated
transciptional factor enters nucleus and binds with DNA to begin transcription

Question 15

what is epigenetics?

Answer 15

environmental factors that can cause heritable changes in DNA with affecting base sequence

Question 16

what is epigenome and what do is do?

Answer 16

DNA and histones is covered in chemical tags. These chemical tags form a secondary layer called epigenome. Epigenome determines the shape of DNA /histone complex.
epigenetic silencing - it keeps genes tightly packed and therefore it cant get read
it can also do the opposite by unwrapping tightly packed genes and histones so that DNA can be exposed
DNA is fixed but epigenetics is flexible as chemical tags can be affected by environments

Question 17

how does the environment affect DNA?

Answer 17

environnment signal stimulates proteins to carry its messages inside the cell where it is passed onto the nucleus. Here it can attach to specific proteins which can attach to sequences of bases on DNA . Once attached there are 2 possibilities:
acetylation of histones leading to the activation or inhibition of a gene
methylation of DNA by attracting enzymes that can add or remove methyl groups

Question 18

what does a strong/weak association of histones with DNA indicate?

Answer 18

when the association of histones with DNA is weak the DNA histone complex is less condensed this means it is easier for transcription factors to bind and hence begin mRNA production (switching the gene on)
when the associtation of histones with DNA is strong the complex is more condensed making it harder for transcription molecules to bind. This can occur do decreased acylation of histones or methylation of DNA.This essentially turns the gene off

Question 19

how does acylation increase/decrase association?

Answer 19

acylation is the process of acetyl group being added to a molecule from acetylcoenzyme A.
acylation decreases positive charges on the histone making it more attracted to phosphate group. Making the complex more condensed and hence harder for transcription factor to bind .(turning the gene of)

Question 20

how does methylation affect DNA

Answer 20

methylation is the process of adding methyl to cytosine. This makes transcription factors unable to bind to the DNA (turning the gene of)
methylation also attracts proteins that condense the DNA- histone complex (inducing deacylation of histones) make it inaccessible to transcription factors

Question 21

what are the 2 types of tumours?

Answer 21

malignant-cancerous

benign - non cancerous

Question 22

how does RNA interference affect gene experssion?

Answer 22

enzymes cuts larger RNA into smaller siRNA (interefering RNA)
one of the 2 siRNA strands combines with the enzyme
the siRNA molecules guides the enzyme to mRNA by paring its bases with complementary ones
the enzyme cuts mRNA into small pieces
the mRNA is longer able to be translated into a polypeptide
this means the gene has not been expressed

Question 23

charicteristics of malignant tumour?

Answer 23

can grow very large
grow rapidly
cell nucleus larger and appears dark due to abundance of DNA
cells become dedifferrentiated
cells dont produce adhesion molecules so can spread(metastasis) forming
not surrounded by capsule so can grow finger like projections into surrounding tissue
secondary tumours
life threating
has whole body effect
more frequently reoccur after removal

Question 24

characteristics of benign tumour>

Answer 24

large size
grow slowly
cells are often differntiated
cells produce adhesion molecules no secondary tumours/spreading
form capsule 
less life threatining
localised effect
rarely reoccur after removal

Question 25

what are tumours derived from

Answer 25

a single mutant cell which uncontrollable mitosis . Then a further mutation that causes cells to become different in growth and appearance. The 2 main genes that play apart are oncogenes and tumour suppressant genes

Question 26

what are oncogenes

Answer 26

mutations of proto oncogenes(stimulates cells to divide when growth factors attach to protein receptor on cell surface membraene ) if proto oncogenes are mutated it can cause them to be permenantly on this happens as : the receptor protein is permentantly activated so growth factor isnt required the oncogene may code for growth factor that is produced in excessive amounts this results in cancer

Question 27

what are tumour suppressor genes

Answer 27

tumour suppressor genes slow down cell division,correct mistakes and do apostasis (programmaed cell death) normally they prevent tumours however if their is a mutation it becomes turned off.Therefore cells can grow out of control.The mutated cells that are formed are usually structurally and functionally different .these can clone themselves and form tumours.

Question 28

what are tumour suppressor genes

Answer 28

tumour suppressor genes slow down cell division,correct mistakes and do apostasis (programmaed cell death) normally they prevent tumours however if their is a mutation it becomes turned off.Therefore cells can grow out of control.The mutated cells that are formed are usually structurally and functionally different .these can clone themselves and form tumours.

Question 29

how does hypermethylation lead to cancer?

Answer 29

methyl group attaches to specific reigon on tumour supression gene DNA this causes transcription factors to be unable to bind making tumour supression gene inactive turned off this causes cells to continue growing and forming tumours

Question 30

what are the effects of oestrogen on breast cancer?

Answer 30

oesteogen regulating the menstrual cycle in women after menopause women are more likely to get breast cancer . fat cells in the breast produce more oestrogen triggering tumours. once a tumour has developed it further increases oestrogen concentration leading to tumour development.Also white blood cells are drawn to the tumour increasing oestrogen production. leading to even greater tumour production it produces the tumour as oestogen has the ability to bind to genes essentially turning them on allowing transcriptional factors to bind. If it turns on proto onco genes to onco genes it will cause a tumour

Question 31

what is the advantage of knowledge of the proteome of organisms like bacteria?

Answer 31

the identification of these proteins that act as antigens on the surface of human pathogens. these antigens can be used as vaccines against diseases caused by pathogens

Question 32

what is the whole genome shotgun technique?

Answer 32

researchers cutting the DNA into many small sections and using computers to align overlapping segments across the genome

Question 33

describe the general process of using DNA technology of gene transfer and cloning to make a protein

Answer 33

isolation of the DNA fragment insertion of the dna fragment into a vector transformation - transfer of dna into suitable host cells identification of the host cells that have taken in the gene by gene markers cloning of the host cell

Question 34

what recombinant DNA technology?

Answer 34

allows genes to be manipulated altered and transferred from one organism to another

Question 35

what are the methods of isolating genes and producing DNA fragments

Answer 35

conversion of mRNA to cDNA using reverse transcriptase using restriction endonuclease to cut fragments containing the gene creating the gene in a gene machine

Question 36

how does reverse transcriptase isolate a gene and its advantage

Answer 36

A desired protein is selected this protien shold have a lot or mrna reverse transcriptase enzyme binds mrna to DNA complementary bases this creates cDNA single stranded DNA double stranded DNA is formed using cDNA template and DNA polymerase the advantage is that it is intron free as DNA based of mrna

Question 37

describe how using restriction endonucleases work?

Answer 37

restriction endonuclease are enzymes that cut up viral DNA at a particular sequence callled a recognition sequence if this occurs at 2 opposite base pairs it leaves blunt edges otherwise it leaves exposed base pairs leaving sticky ends sticky ends are better as they allow the DNA to easily reconnected to the DNA

Question 38

describe the gene machine works?

Answer 38

desired proteins nucleotide sequence is worked out and fed into computer sequence is checked for biosafety/biosecurity and ethical requirements computer designs and assembles small single strands of nucleotides called oligonucleotides which can be assembled into desired gene oligonucleotides joined to make a gene which is replicated and made double stranded by adding nucleotides using polymerase chain reaction using sticky ends the gene can be inserted into bacterial plasmid genes are checked

Question 39

what is the use for sticky ends?

Answer 39

the single stranded end from one fragment can be joined another single strand end from another fragment. Once the complementary bases bond DNA ligase is used to bind the phosophate - sugar backbone

Question 40

what are the way in which DNA is cloned?

Answer 40

in vivo - transferring the fragments to a host cell using a vector in vitro using the polymerase chain reaction

Question 41

how is DNA fragement prepared for insertion?

Answer 41

addition of extra lengths of DNA RNA polymerase must attach to DNA near gene in reigon called promoter nucleotide base of promoter attaches to RNA polymerase and transcription factors and transcription starts #

Question 42

how is DNA fragment inserted into a vector

Answer 42

vector transports DNA into host cell this is usually done by plasmids plasmids are circular lengths of DNA restriction endonucleases (same enzyme used to cut up DNA fragment)is used to break up circular lengths of DNA of plasmid this means it cuts at the same sequence of bases sticky ends of plasmids is complementary to sticky ends of DNA they are combined and the enzyme DNA ligase is used to cataylse phosphodiester bonds

Question 43

how is DNA introduced to host cells ?

Answer 43

In a process called transformation plasmids and bacterial cells being mixed together in a medium containing calcium ions. Calcium ions and in heat shock make the bacterial membrane more permeable allowing plasmids to pass through into cytoplasm. this is not always possible as only a few bacteria take up plasmids some plasmids will close without incorperating the DNA sometimes DNA fragments join together to form its own plasmids

Question 44

what are the three methods used to test wether DNA has sucessfuly entered the plasmid

Answer 44

antibiotic -before adding the dna to the plasmid add resistance to tetracycline and resistant to ampicillin genes. Add the DNA fragment inbetween the tetracycine so its no longer functional. Grow plasmid to agar plate. Transfer the bacterial colonies to a plate with ampicillin. Out of those colonies that survive transfer them to tetracyline plate. Those colonies that are alive on the ampicillin plate and are dead on tetracycilne have the DNA fragment succesffuly added fluorescent markers- DNA fragment added inbetween GFP fluorescent gene on DNA fragment making it unfunctional.this means all the non glowing colonies are recombinant lactase marker - DNA fragemnt added inbetween lactase enzyme gene making it unfunctional. lactase can turn substance colourless to blue. colonies which cannot turn the substance blue contain recombinant DNA

Question 45

what are the stags of poylmerisation chain (in vitro)

Answer 45

1) DNA fragment,primers and DNA polymerase are placed in a vessel in the thermocycler at 95c causing two strands of the DNA fragements to seperate due to hydrogen bonds breaking 2) mixture is cooled to 55c causing primers to bond to their complementary bases at the end of the strand. the primers provide the starting squences for DNA polymerase to begin copying as DNA polymerase can only attach to nucleotides at the end of DNA 3) temperature is increased to 72c. this is optimum temperature for DNA polymerase to add complementary nucleotides along each of the seperated DNA strands.It begins with the primer at each strand and adds nucleotides until the end of the chain

Question 46

what are primers,thermocyclers ?

Answer 46

primers short sequences of nucleotides that have a set of bases complementary to those at the end of DNA fragments thermocyclers- computer that varies temperature over a time

Question 47

advantages of in vitro/in vivo?

Answer 47

in vitro - extremely rapid does not require living cell in vivo - introduced genes into another organims no risk of contamination

Question 48

what are DNA probes?

Answer 48

DNA probes are short single stranded nucleotides sequences that are complementary to the mutation/disease we are lloking for. They are radioactive/fluorsecent.

Question 49

how are DNA probes used to locate genes?

Answer 49

fragment of DNA produced complementary to the DNA sequence of mutation/disease DNA probe clones using polymerase chain reaction marker e.g fluorscent dye is added to the DNA probe DNA of allele is heated to break hydrogen bonds and seperate strands seperate strand is cooled in a mixture with DNA probes if DNA contains mutant allele it will bind with DNA probe and hence show fluroscent label the fluorscent label can be checked via microscope

Question 50

what are the advantages of genetic screening?

Answer 50

allows for personalised medication as doctors can knows diseases within genotype councelling can discuss wether offspring will have disease ect

Question 51

what is VTNR

Answer 51

variable number tandem repeats- unique non coding DNA reigon for every person. the chance of 2 people having the same VTNR is extremely unlikely

Question 52

what is gel electrophoresis?

Answer 52

used to seperate DNA fragments according to size DNA fragment is placed on agar plate and voltage is applied across it. resistance of the gel means larger fragments move more slowly over time smaller fragments move across meaning

Question 53

how are genetic fingerprionts made?

Answer 53

extraction - Get DNA from blood sample /hair ect quantinty can be increased with polymerase chain reaction. digestion - cut into fragments by restriction endonuclease segregation - fragments seperate by gel electrophesis and voltage then immersed in alkali to seperate 2 strands to 1 hybridisation - fluorscent or radioactive DNA probes which have complementary base sequences to VTNR bind to eachother development - X-ray film is put over the nylon membrane.film is exposed by radiation from the DNA probes .Series of bars is revealed

Question 54

what are the uses of DNA fingerprinting?

Answer 54

can be used for paternity test as child DNA fingerprint should be same as mother /father DNA can be matched at a crime scene plant and animal breeding to stop undesirable traits

Question 55

2 types of gene therapy?

Answer 55

somatic; allelea in body cell are altered and not passed on | germline: alleles in sex cells are altered and passed on

Question 56

what is gene therapy?

Answer 56

when alleles are altered to treat disease can happen through adding a healthy allele and inserted into cells using vectors if mutant alleles are dominant they can be silenced by adding DNA in the middle