Topic 8A - Mutations and Gene Expressions

Question 1

Why might addition mutations cause major changes to a protein, and why might it not?
(3)

Answer 1

Addition mutations result in frame shifts if there are one or two bases added. All triplet codes to the right will alter, therefore changing the amino acid sequence / primary structure of the protein. If there are three additions close together, only a small section is layered / potentially only the addition of one amino acid.

Question 2

Describe what is meant by induced pluripotent stem cells.

Answer 2

• and they are unspecialise

Induced pluripotent stem cells are pluripotent stem cells formed from unipotent stem cells / somatic / body cells. (1)
They are formed by using transcription factors to stimulate. (1)

Question 3

note

Answer 3

tightly condensed histones may make a gene hard to access due to lack of acetylation, and so is inactive / switched off.

Question 4

What are silent mutations?

Answer 4

mutation that doesn’t cause a change in amino acid order

Question 5

All types of mutations

Answer 5

substitution, deletion, addition, duplication, inversion, and translocation (within same or to diff chromosome)

• some of these cause a frameshift downstream of the mutation

Question 6

What can cause epigenetic changes? Are they permanent?

Answer 6

The environment and lifestyle.
Most epigenetic markers removed during gamete formating, out some may be passed on.
Chemical tags can be removed, so aren’t permanent.

Question 7

epigenetics

Answer 7

How chemical tags attached to DNA (and histones) that affect gene expression without altering the base sequence

Question 8

What is the impact of methylation on DNA (… transcriptional factors?)?
How is gene expression impacted?

Answer 8

Adding methyl group allows it to bind to CpG binding site - which is a promoter region (found between C and G bases). So, the site is now not complementary to transcriptional factors :
can’t bind, so RNA polymerase can’t bind - transcription inhibited.

Adding methyl = gene switched off
Removing methyl = gene switched on

Question 9

How does acetylation affect DNA?
How is gene expression impacted?

Question 10

Tumour suppressor and proto - oncogenes - think about how these are impacted by methylation

Answer 10

Adding methyl / hypermethylated - binding site changed on gene promoter region - TF and RNA polymerase can’t bind - tumour suppressor protein not transcribed and translated.
cell division is uncontrolled, so lead to tumour growth.

Hypomethylation/ removing methyl groups

Question 11

Gene mutation

Answer 11

change in DNA base sequence ( spontaneously) mainly during DNA replication

Question 12

What do mutagenic agents do?

Answer 12

Increase the rate / likelihood of mutation
- may change sequence and encoded polypeptide chain then & different primary structures as different hydrogen (ionic and disulfide later on) formed as R groups interact differently > tertiary structure altered may mean non-functional protein
- mutations in genes for cell cycle may cause cancer

Question 13

degenerate code

Answer 13

All organism’s DNA contains the same 4 type of bases and so multiple triplets can code for the same amino acid

Question 14

Which mutations are least and most harmful?
Note some mutations are hereditary if gamete has it, and some mutations can cause genetic disorders or increase chance of cancer.

Answer 14

Least: substitution and inversion, which may only change a couple of codons, degenerate may mean no impact.

All others cause a frameshift in gene downstream : may result in incomplete triplets, stop codon earlier on, completely different protein made.
- Translocation may change phenotype

Question 15

3 types of mutagenic agents

Answer 15

1. Chemicals called base analogs can substitute for another new base during DNA replication (so mention how it can pair with the complementary base to the one its substituting !)
2. some chemicals can delete /alter bases (e.g. adding a chemical group to change its structure - methyl probably an example)
   * Example to know : Alkylating agents add alkyl group to guanine, changes structure so not complementary
3. Radiation (UV) can change DNA structure - problems then arise w/ structure or during replication

• Link all of these to changing base sequences and transcription/ translation

Question 16

note

Answer 16

only part of the totipotent DNA is expressed / translated when cells become more specialised and only some genes are expressed to be able to carry out specialised cell function
- example: in RBCs the gene for the presence of a nucleus must be switched off

Question 17

Stem cells

Answer 17

Undifferentiated cells that continually divide to become specialised,process: differentiation

Question 18

Totipotent stem cells

Answer 18

can mature and divide into any type of body cell - including placenta cells
These only occur for a limited time in (mammalian) embryos.

Total power

Question 19

pluripotent stem cells
*

Answer 19

Also in embryos and can divide in unlimited numbers.
- not into placenta cells

• can be used in treating human disorders

Question 20

multipotent stem cells

Answer 20

found in mature mammals can divide to form a limited number of different differentiated cells

Question 21

unipotent stem cells

Answer 21

Stem cells that divide into one type of cell - must know example of cardiomycytes (circulatory/ nervous/ immune system)

Question 22

Example of uni potent stem cell and why is it important that they are Unipotent.

Answer 22

Skin epidermal cells.
They have to divide quickly to regenerate damaged tissue - nature decreases risk of tumour development as only a few genes to transcribe (e.g. gene for haemoglobin is switched off)

Question 23

What does it mean for a cell to be specialised

Answer 23

During their development, they only transcribe/late part of their DNA. Under certain conditions, gives may be switched off or on (read revision guide on stem cells)

Question 24

bone marrow stem cells produce…

Answer 24

blood cells

Question 25

Benefits of using stem cells in medicine?

Answer 25

Could save many lives - like growing organs Could improve quality of life - eg, replace cells in eyes to cure blindness - there may be more (such as laws against cloning or growing embryos past certain days - try exam questions)

Question 26

3 main sources to obtain human stem cells

Answer 26

1. Adult stem cells from bone marrow/ body tissue, simply done but they aren't as flexible as embryonic stem cells as multipotent - specialise into a few. 2. Embryonic stem cells at early stage using IVF (grown in lab, stem cells removed and embryo destroyed), flexible as pluripotent. 3. Induced pluripotent stem cells (see other cards)

Question 27

role of a tumour suppressor gene

Answer 27

To slow down cell division or the cycle, or to cause cell death if error during DNA replication detected - hyper methylation of the gene stops cell destruction when needed

Question 28

Cardiomyocytes

Answer 28

heart muscle cells that don't divide in mature mammals. Research suggests some regeneration via small supply of unipotent stem cells/cardiomyocytes in heart. - debate on whether it happens and how often in lifetime

Question 29

stem cell therapy example

Answer 29

For diseases affecting blood and immune/lymphatic system > bone marrow transplants where faulty stem cells are removed completely and new ones put into bone marrow to specialise and produce healthy blood cells. HAS BEEN SUCCESS TO TREAT SOME CANCERS.

Question 30

Examples of other diseases that may eventually be treated by stem cells

Answer 30

Spine injuries to replace nerve tissue Heart disease/damage by heart attacks - replacing tissue Stem cells to grow whole new bladders to be implanted as replacements >aka organ transplants too

Question 31

Benefits of stem cells

Answer 31

- save many lives (organ donation when waiting list long) - improve quality of life, like replacing damaged cells in eye for those blind etc

Question 32

3 sources of stem cells scientists could use, and desc. them a bit.

Answer 32

1. somatic/adult stem cells: from bone marrow using simple operation with little risk but high discomfort. Aren't as flexible as other options as multipotent 2. embryonic: only obtained at early stages of development when developed in lab (IVF, fertilised outside of womb). At 5 days, stems removed and embryo destroyed. V. flexible - unlimited division and pluripotent 3. induced pluripotent: see other cards

Question 33

describe iPS process of reprogramming adult stem cells into pluripotent ones

Answer 33

1. Isolate sample of cells from adult (like skin) and grown in dish. 2. Treat cells with appropriate T factors (which are proteins) that cause somatic cells to express all genes associated with pluripotent stem cells, so can specialise later. [Extra: one way to introduce TF is to infect w/ modified virus that has genes coding for the TF needed. When infected, genes can be passed onto adult cell's DNA, so itself can then produce the TF needed to express associated pluripotent genes] 3. Wait a few weeks 4. Change culture conditions to stimulate cells to differentiate into variety of cell types, like cardiac muscle cells.

Question 34

Booklet says...

Answer 34

Cardiomyocytes are unipotent and are muscle cells responsible for contracting ventricle walls. - watch clips to see why they have lots of mito and why they are called unipotent

Question 35

Ethical issues of stem cells

Answer 35

- destruction of embryo that has potential and right to life - some think it's better to obtain stem cells from unfertilised eggs, but artificially activated to start dividing (wouldn't survive many days if placed in womb as foetus) - some think only somatic stem cells should be used, but not as flexible - iPS probably the best as they are flexible - especially if obtained from same patient so little chance of rejection as genetically identical

Question 36

How is gene expression controlled in eukaryotes?

Answer 36

Transcriptional factors that move from the cytoplasm and bind to promoter regions of DNA / before genes to either inhibit or stimulate transcription (examples include oestrogen, steroid hormones)

Question 37

2 ways/reasons why T factors may be stopped from binding to their respective promoter regions?

Answer 37

1. competitive and non-comp. substances/inhibitors bind to promoter region either instead/possibly changing the shape. 2. mutation in DNA sequence either changes promoter region on the DNA or changes the amino acid sequence that is translated for the TF > shape changes >not complementary binding sites

Question 38

promoter region

Answer 38

a section of the DNA base sequence that controls the transcription of a gene / binding site for TF, located upstream to the gene where proteins bind (RNA polymerase, TF)

Question 39

note about activators and inhibitors

Answer 39

practically all eukaryotic cells need activators to begin transcription, but prokaryotes don't really

Question 40

explain how activators and repressors AS TRANSCRIPTIONAL FACTORS work in relation to transcription

Answer 40

Activators: bind to promoter region and then to TF alongside, then RNA polymerase binds encouraging/ increase RATE transcription of the gene into pre-mRNA then MRNA Repressors: bind to promoter region to block it and TF are unable to bind to repressors, so preventing/ DECREASE THE RATE of them and RNA polymerase binding and transcribing etc - TF help control the shape of the binding site too for RNA polymerase

Question 41

describe how oestrogen activates transcription of a particular protein

Answer 41

1. it's lipid soluble molecule so simple diffuse across phospholipid bilayer into cytoplasm 2. a receptor is naturally attached to a TF which are both bound to an inhibitor > oestrogen can bind to elsewhere on this receptor. 3. Oestrogen causes receptor to change shape and release inhibitor, LEAVING the TF's DNA binding site exposed 4. TF can move via nuclear pore and towards promoter region to begin process of transcription (mention RNA polymerase) > to produce pre/mRNA.....protein

Question 42

what might replace oestrogen

Answer 42

a drug that may act as a competitive inhibitor - oestrogen itself acts a bit like a non-competitive inhibitor to the inhibitor molecule

Question 43

why oestrogen affects transcription of some genes in some cells only

Answer 43

- only some receptors have a complementary binding site for it - aka only cells with oestrogen receptors allow it to bind

Question 44

TF doesn't bind, it means

Answer 44

inactive gene

Question 45

how can TRANSLATION of mRNA be controlled

Answer 45

destroyed using interfering RNA/RNAi - such as siRNA small interfering RNA can cause an RNA interferance/silencing

Question 46

what is siRNA

Answer 46

short double-stranded (m)RNA

Question 47

describe the process of siRNA acting: miRNA works in a similar way in PLANTS

Answer 47

1. mRNA transcribed and leaves nucleus to cytoplasm. 2. enzyme/proteins cuts the mRNA into one siRNA single stranded piece that it complementary to an EXACT mRNA sequence (other siRNA strand degraded) 3. siRNA AND its associated proteins/enzymes binds to target mRNA molecule by complementary base pairing. 4. associated proteins cut/HYDROLYSE the mRNA into fragments to not be translated. 5. mRNA fragments moved into processing body to be degraded - SUCH AS lysosome and its enzymes

Question 48

advantage of siRNA (describe one of them a bit more)

Answer 48

- no impact on DNA sequence - could be used to treat genetic disorders, stopping mRNA from being translated into some proteins (e.g. ones that aid in cell division if it's occurring too quickly and creating tumours) > viruses could be used to deliver siRNA as it could replace the viral RNA [then you'd also have to add complementary receptors to the target cells]

Question 49

what is RNAi

Answer 49

small sections of non-coding RNA

Question 50

describe how miRNA works in most mammals (benefit is included in explanation)

Answer 50

(similar beginning part to siRNA to set the scene) 1. miRNA not usually fully complementary, like siRNA, to target gene BUT so can target more than one mRNA molecule 2. It also, likewise, associates with proteins and both bind to mRNA w/ complementary base pairing (H bonds formed) in CYTOPLASM! 3. this time, the miRNA-protein complex physically block translation of the target mRNA 4. mRNA moves to processing body where degraded or stored for translation later...

Question 51

difference in origin of siRNA and miRNA

Answer 51

siRNA is man-made, basically all miRNA in eukaryotes is produced by cells for the purpose of gene silencing (where the mRNA is being transcribed, it cannot be translated into the protein)

Question 52

effects of gene mutations

Answer 52

> can be no effect (especially when in non-coding genes), beneficial or harmful as introduce new alleles

Question 53

causes of gene mutations

Answer 53

spontaneous mutation during replication (errors from DNA polymerase), or they can be induced mutations due to mutagens - these mutations can happen in section of DNA (changing structure or function) or in a whole chromosome section

Question 54

epigenetics note

Answer 54

only in eukaryotes we look at

Question 55

epigenome

Answer 55

The chemical/epigenetic markers or tags that attach to your DNA which can change the expression of genes, BUT do not alter base sequence > influenced by your environment, but some can be inherited - acetylation and methylation

Question 56

how acetyl and methyl affect DNA epigenome > describe

Answer 56

Acetyle binds to histones! adding acetyl affects winding of histones by making DNA wrap around them less tightly. Less condensed = easier for TF factors to bind, so increases transcription. methyl binds to CpG site (found between cytosine and guanine). If methyl has been added/bound to promoter region of DNA then transcription is inhibited as the shape of DNA has changed and no longer complementary to TF'S binding site for it. This also means RNA polymerase won't attach etc.

Question 57

info on epigenetic markers

Answer 57

- sleep, diet, exercise, aging, emotional trauma can cause changes in epigenetics - most markers are removed during gamete formation, some evidence they still get passed on

Question 58

how do they regulate gene expression: epigenetics vs RNAi

Answer 58

epi: inhibits or promotes transcription of genes via chemicals RNAi: inhibits gene expression after transcription

Question 59

why is RNAi referred to as gene silencing?

Answer 59

- cuts mRNA so not translated - while the structure of the DNA base sequence of gene remains the same, only stops translation

Question 60

in reference to epigenomes, briefly state what causes cancer

Answer 60

hypermethylation or lack of / hypoacetylation of its histones of tumour suppressor genes

Question 61

benign vs malignant tumours. - benign can become malignant

Answer 61

benign: not cancerous, slower growth, covered in fibrous tissues to not spread, often harmless but can cause blockages or put pressure on organs malignant: cancerous, faster growth, cells can break off and spread via blood/lymphatic system

Question 62

appearance of tumour cells against normal cells

Answer 62

Tumours divide faster by mitosis and more frequently therefore. - nucleus is larger/darker (may be more than one) - irregular shape - different agents - don't produce all proteins needed to function correctly - don't respond to regulatory processes / proteins

Question 63

describe the hypomethylation of proto-oncogenes

Answer 63

Less / removal of methyl groups on the promoter region of proto-oncogene means means the binding site for TF and RNA polymerase is exposed (site no longer changed), more frequent binding > speeding up transcription. More proteins of the gene are coded and leads to uncontrolled cell division (tumour) / mitosis

Question 64

which cells express proto-oncogene

Answer 64

skin and epithelial cells in small intestine, as need to divide quickly / more frequently