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M8 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What are the 4 mutations that alter the sequences of the bases in DNA other than substitution and deletion?

A

Addition - adding an extra nucleotide.

Inversion - group of nucleotides becomes separated from the DNA sequence and rejoins in the same place but in reverse order.

Duplication - one or more nucleotides are duplicated - frame shift.

Translocation - group of nucleotides becomes separated from DNA sequence of one chromosome and becomes inserted into the DNA sequence of a different chromosome.

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2
Q

What happens to the DNA when cells differentiate?

A

DNA that is not required for its specific function is shut down by being wrapped tightly around histone proteins. DNA that IS required is wrapped loosely around histone proteins.

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3
Q

What might stem cells be used for?

A
  • Testing drugs on human cells (before clinical trials)
  • Generate tissues for transplantation
  • Understand how to prevent and treat birth defects.
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4
Q

What are the pros and cons of using stem cells?

A

PROS
+ may be used to cure diseases
+ may be used to avoid tissue rejection in transplanted cells/organs
+ could be used to test experimental drugs
+ Can be studied to better understand how disease develops
+ Capable of self-renewal

CONS
- religious/ethical debate about stem cells harvested from embryos
- possible unintentional spreading of viruses/infections
- possibility they may become cancerous
- correctly directing differentiation can be difficult

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5
Q

What are the names given to cells that are able to :
1. give rise to any cell type and make a whole organism
2. give rise to any cell type but not make a whole organism.
3. give rise to several cell types but not all
4. differentiate only into a single cell type

A
  1. Totipotent
  2. Pluripotent
  3. Multipotent
  4. Unipotent
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6
Q

Where do totipotent, pluripotent and multipotent stem cells come from?

A

Totipotent = single celled embryo
Pluripotent - embryonic stem cells
Multipotent = ‘adult’ stem cells, placental stem and core blood stem cells

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7
Q

What are transcription factors?

A

Specific moelcules that have a site that can bind to a specific base sequence on DNA in the nucleus, enabling RNA polymerase to bind and innitiate transcription.

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8
Q

What are activators and repressors?

A

Activators and repressors combine with transciption factors to change the shape of its DNA binding site.

Activators = allow it to bind (switching genes on)

Repressors = prevent it from binding (switching genes off)

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9
Q

What is oestrogen and what does it do to DNA?

A

Oestrogen is a steroid hormone (lipid derived) so is lipid soluble. It acts as an activator.
It circulates in the blood and diffuses across plasma membranes of all cells.

  • Oestrogen binds with a receptor site attached to a transcription factor.
  • The binding of oestrogen and receptor forms an oestrogen-oestrogen receptor complex.
  • This changes the shape of the DNA binding site of the transcription factor.
  • This enters the nucleus through the nuclear pores and binds to a specific base sequence in the DNA.
  • This causes RNA polymerase to bind to the DNA and begin transcription.
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10
Q

What is the epigenome?

What happends after fertilisation and how does this affect twins?

A

A series of molecular tags that regulate gene transcription and can be altered by environmental factors.

After fertilisation most of the epigenetic markers are wiped from the DNA so identical twins will be similar at birth but aquire different epigenetic markers over their lifetime.

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11
Q

Name the 2 epigenetic tags - do they switch genes on or off?

A

Acetylation of histone proteins - switch on

Methylation of DNA - switch off

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12
Q

Describe methylation of DNA

A

Cytosine bases are more or less methylated by the addition or removal of CH3 groups.

THis makes it more or less difficult for transcription factors to bind to the DNA.
The more methylated, the more difficult for transcription factors to bind so gene is switched off.

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13
Q

Describe Acetylation of Histone Proteins

A

Addition or removal of acetyl groups changes the charge on the histone proteins, changing the association between DNA and histones making it wind more or less tightly.

e.g. More acetylation - histones more negative and so DNA wrapped more loosely (because it repels the negative charge). Switching the gene on.

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14
Q

Define epigenetics

A

the heritable changes in gene function without changes to DNA sequence.

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15
Q

What is RNA interference?

A

A process in which RNA molecules inhibit gene expression by causing the destruction of specific mRNA molecules and thus prevent translation.

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16
Q

What are the 2 types of RNA that cause RNA interference? What are their structures?

A

microRNA (miRNA) :
molecules fold back on themselves forming a hairpin structure

Small interfering RNA (siRNA):
short and double stranded molecule.

BOTH are relatively small (20-25bps)

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17
Q

What is the mechanism for siRNA?

A

1) An enzyme cuts large double stranded RNA molecule into small sections of siRNA.
2) One of the two strands of siRNA combines with an enzyme.
3) The siRNA molecule guides the enzyme to an mRNA molecule by binding to complementary sequences on the mRNA molecule.
4) The enzyme cuts the mRNA into small sections.
5) The mRNA is no longer translated into a polypeptide
6) Gene expression has been blocked.

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18
Q

Describe micro RNA.

A
  • Found only in mammals.
  • Not fully complementary so may target >1 mRNA molecule.
  • miRNA blocks translation rather than cutting mRNA into fragments.
  • The mRNA is moved to a ‘processing body’ where it is either degraded or stored for later use.
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19
Q

What is a Benign and Malignant tumor? What is Metastasis?

A

Tumor: group of cells dividing in an uncontrolled way.

Benign: A mass of abnormal cells that develop when there is no need for growth or repair.

Malignant: A tumor that tends to spread to other parts of the body via the blood or lymph systems.

Metastasis: When a secondary tumor forms.

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20
Q

In what 2 genes do the initial mutations occur that lead to cancer?

A

Tumor Suppressor genes and Proto-oncogenes.

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21
Q

How do Tumor Suppressor genes usually work? What happens to mutated TS genes?

A

Tumor Suppressor genes produce a growth-inhibiting protein.

If DNA damage is detected or the cell cycle has not been correctly completed, the cell cycle will stop at the checkpoint.

Mutated TS genes allow the cell cycle to continue even in the presence of mutated DNA.

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22
Q

What are Proto-oncogenes? What happens when these are mutated? What are they called?

A

The cell cycle is controlled by signals that tell the cell that it needs to divide if there is a need for growth and repair.

Proto-oncogenes produce proteins that control these signals.

Mutated Proto-oncogenes = Oncogenes

Oncogenes leads to uncontrolled cell division, when division is not needed for growth or repair.

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23
Q

What are the two types of Oncogenes that can arise?

A
  • Mutation of gene that codes for the cell surface receptor so that it is permanently switched on - even in the absence of growth factors.
  • Mutation in the gene that produces growth factor so that too much growth factor is produced.
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24
Q

Describe 3 ways that hypermethylation can lead to tumors / uncontrolled division.

A

Hypermethylation of promotor sites of Tumor suppressor genes can cause them to be inactivated - allowing cell division even when DNA is damaged.

Hypermethylation of promoter sites of DNA repair genes can inactivate normal DNA repair enzymes.

Hypermethylation of oncogene promotor sites can cause oncogenes to be activated.

25
Q

Drug treatments have been developed that ____ enzymes involved in histone ________ or DNA _________. These drugs can reactivate genes that have been silenced such as tumor suppressor genes.

Some cancer treatments aim to _____ the action of ___________. (e.g. by blocking receptors in some cases)

A

inhibit
acetylation
methylation

block
oestrogen

26
Q

What are the uses of recombinant DNA technology?

A

1) Transfer genes into bacteria to make useful products (e.g. insulin).
2) Transfer genes into plants and animals so they can aquire new characteristics (e.g. disease resistance).
3) Transfer genes into humans (Gene Therapy) so they no longer suffer from genetic diseases (e.g. cystic fibrosis).

27
Q

Name the 5 steps of Recombinant DNA technology (In vivo)

A

1) ISOLATION of DNA fragments which include gene required for replication.
2) INSERTION of the DNA fragments into the vector (e.g. plasmid).
3) TRANSMORMATION - the introduction of the vector into a suitable host cell.
4) IDENTIFICATION of the host cells that have successfully taken up the gene (by gene markers).
5) GROWTH or cloning of host cells.

28
Q

Name the 3 methods of Isolating DNA fragments (In vivo)

A

Reverse transciptase
Restriction Endonuclease
Gene Machine

29
Q

Decribe the process of Reverse transcription.

A
  1. Cells which synthesise and secrete the required product will contain large quantities of this particular mRNA in the cytoplasm. (e.g. mRNA for insuline gene extracted from B cells in the Islets of Langerhans (in pacreas).
  2. Use of Reverse Transcriptase (isolated from retroviruses) to produce DNA from this mRNA.
  3. Single strand of DNA is called complementary DNA (cDNA). This is produced and isolated using enzymes.
  4. The enzyme DNA polymerase converts cDNA into double stranded DNA.
  5. This DNA is then inserted into a plasmid vector.
30
Q

Describe the use of Restriction Endonuclease.

A

Restriction Endonuclease is used to cut a fragment containing the desired gene from DNA.
- A variety of enzymes recognise a specific palindromic base sequence (same forwards and backwards) and cut the DNA at this point.
- Some cut the DNA straight across to produce blunt ends and others cut it staggered to produce sticky ends.
- Sticky ends allows complementary overhangs to allow insertion of this DNA into a other DNA.

31
Q

Describe the Gene Machine.

A

1) Amino acid sequence of required protein is determined and from this the mRNA and DNA triplets worked out.
2) Sequence of nucleotide bases is fed into the computer.
3) Checked for biosafety to international standards.
4) Small overlapping sections of DNA called OLIGONUCLEOTIDES are designed.
5) Each oligonucleotide is assembled base by base into the required sequence.
6) These are then put together to make the gene WITHOUT ANY INTRONS.
7) This is made double stranded (with sticky ends) and replicated using PCR.
8) Checked for accuracy using sequencing techniques and those with errors rejected.
9) Can then be inserted into a plasmid to be used.

32
Q

What is the difference between In vitro and In vivo cloning?

A

In vitro - using PCR

In vivo - transferring gene into host cell using vector

33
Q

How are DNA fragments prepared for insertion? (What is added?)

A

DNA fragment prepared for insertion by adding:

  • Promoter (DNA sequence where transcription factors and RNA polymerase can bind).
  • Terminator (DNA sequence which releases RNA polymerase).

…With restriction endonuclease.

34
Q

Describe Insertion (In vivo cloning)

A

DNA fragment (with promoter and terminator) is inserted into plasmid vector:
- Restriction endonuclease leaves complementary sticky ends.
- These fragments can then pair up and join using DNA LIGASE producing recombinant DNA.

35
Q

Describe Transformation (In vivo cloning)

A

Transformation = reintroduction of plasmids into host bacterial cells.

Calcium Chloride and heat shock is a common method.

Not all cells will take up the recombinant plasmids.

36
Q

Describe Identification (In vivo cloning)

A

Identification of recombinant bacteria is essential.

You must be able to distinguish recombinant plasmid from original plasmid - using REPLICA PLATING.
Marker genes are used (e.g. antibiotic resistance).
Bacteria grown on plates containing antibiotics- any bacteria without resistance gene / plasmid will die and not form colonies.

Once the recombinant bacteria have been identified, they can be cultured in a fermenter on the industrial scale. The gene products can be extracted and purified.

37
Q

Describe and explain Replica Plating.

A

You must be able to distinguish recombinant plasmid from original plasmid - using REPLICA PLATING.

The desired gene is inserted into the original plasmid (with Antibiotic A and B resistance).
This interferes with B resistance gene so the bacteria is no longer resistant to antibiotic B.

All bacteria are grown on normal agar.
A replica of this original plate is taken to ONOCULATE 2 other plates - each containing an antibiotic.

Plate 1 (antibiotic A) - bacteria that have taken up either original or recombinant plasmids grow.

Plate 2 (antibiotic B) - Bacteria without inserted gene grows.

The bacteria that survive on plate 1 but not plate 2 are have the recombinant plasmids and can be used.

38
Q

Describe the process of PCR.

A

Reactants mixed together in a PCR tube:
- DNA
- DNA polymerase (thermostable)
- Small primer sequences
- Good supply of free nucleotides.

Tube placed in PCR machine.

Mixture heated to 90-95 degrees C for 30s. DNA strands separate as H-bonds break.

Mixture cooled to 55-60 degrees C. Primers bind to DNA strand ends.

Mixture heated to 76 degrees C for 1min - optimum temp for DNA polymerase. DNA replication.

39
Q

What are primers?

A

Sequences of bases that join to the beginning of the DNA strands to allow DNA polymerase to atttach.

40
Q

PCR steps 2-4 can be repeated around __ times to give around __ billion copies of original DNA.

The whole process takes around __ hours - much of this time is spent _______ and _______.

A

30x
1 billion

3 hours
heating and cooling

41
Q

Next Generation Sequencing (NGS)

Sequencing methods are continuously ________ and have become _________.

It is similar to sanger sequencing (old method) in that both techniques sequence _________.

NGS is _____ as millions of fragments can be sequenced in a _____ run and so has a lower ____ per sample.

Sanger is more ________ but only sequences ____ fragment at a time.

A

updated
automated
fragments
faster
single
cost
accurate
one

42
Q

What is Genomics?

What are examples of coding and non-coding DNA in eukaryotes?

A

GENOMICS = the study of genomes

Coding = exons - genes that code for proteins

Non-coding = introns, telomeres, centromeres and regulatory sequences

43
Q

What can be done to determine the sequences of proteins of an organism (proteome)?

Name a possible application of this.

In complex organisms, that can cause complications with translating the genome into the proteome?

A

First determine the genome of simpler organisms.

  • identification of potential antigens for use in vaccine production.

The presence of non-coding DNA and regulatory genes.

44
Q

What are the uses of comparing genomes?

A

1) Genes found in ALL organisms = probably required for fundamental life process

2) Can reveal evolutionary relationships - phylogenetic trees

3) Model organisms can be used to research the ROLES of particular genes - e.g. look at effects of mutations

4) Comparing genomes of pathogenic and non-pathogenic organisms - identify new targets for drugs/vaccines

5) Analyse DNA of individuals to assess risk of dieases and detect if carrier of mutant alleles.

45
Q

Name some benefits and issues of GMOs.

A

+ Herbicide, prest and disease resistance
+ Extended shelf-life
+ Increases growth rate - growth hormone production (animals)
+ Used to produce medicinal drugs (animals)
+ Used to produce medicine (bacteria) e.g. human insulin

  • Pests/pathogens evolving resistance / genes being transferred to pathogens (bacteria)
  • Farmers must repeatedly buy seeds (as don’t reproduce)
  • Transfer of antibiotic resistance to pathogens in intestine of consumer.
  • Most GM animals die during development + harmful side effects
46
Q

What does gene therapy do and how?

A

Gene therapy adds a correct copy of a defective gene.

Gene therapy uses a vector (often viruses) to deliver a gene to the cells where needed. Once inside, the cell uses the information to build RNA and functional protein molecules.

Gene therapy plasmids are sometimes packaged inside liposomes which deliver contents by fusing with the cell membrane.

47
Q

What are the pros and cons of using viral vectors in gene therapy?

A

+ Good at targeting and entering cells.
+ Can be modified so they can’t replicate and destroy cells.

  • Carry a limited amount of DNA and so some genes may be too big to fit.
  • Can cause an immune response: sickness, blocking virus from delivering gene or kill cells once gene is delivered.
48
Q

What are the pros and concs of using liposome vectors for gene therapy?

A

+ Can carry larger genes.
+ Most don’t trigger an immune response.

  • Much less efficient at getting into cells.
49
Q

What do disease candidates need to be for successful gene therapy?

A
  • be caused by a single (or few) genes.
  • be fixed by the presence of a dominant allele (wouldn’t work for disease caused by a dominant allele).
  • have accessible diseased tissue so working genes can get to it.
50
Q

What are the two types of gene therapy

A

SOMATIC CELL GENE THERAPY- theraputic genes transferred into somatic (non-gametic) cells. e.g bone marrow and blood cells. Will not be inherited.
AND
GERM LINE GENE THERAPY - transferred into germ (gametic). Heritable. Not being attempted currently for safety and ethical reasons.

51
Q

Does Somatic gene therapy work and is it safe?

A

Been limited in its success (difficult to get liposomes in) but has had several success stories e.g. treatment of SCID.

LT effects are largely unknown. Concerns that it may lead to cancers forming if inserted gene interferes with activity of tumour supressor gene. Viral vectors may also cause immune, inflammatory or toxic effects.

52
Q

Describe Gel eletrophoresis

A

Tank set up containing agarose gel.

DNA cut into fragments with restriction endonucleases and loaded into wells.
(+ buffer)

Direct current passes continuously through gel.

DNA fragments carry a small negative charge so are pulled through the gel towards the anode.

The smaller the fragments the faster they move through the agarose matrix.

Southern blotting. DNA radioactively labelled (or flueorescent). Autoradiography.

53
Q

What is a probe?

A

A short single-stranded length of DNA that has a ‘label’ attached to it that makes it identifiable.

54
Q

What is DNA hybridisation?

A

When DNA probes with complementary sequences of bases bind to specific alleles.

55
Q

Describe DNA hydridisation.

A
  1. Sequence length of DNA you want to find.
  2. Make a DNA fragments with Gene machine.
  3. Make multiple copies of DNA using PCR.
  4. Heat DNA to seperate strands (or immerse in alkali solution).
  5. Cool and add the DNA probes - will bind to complementary sequences of DNA if allele present.
  6. Wash away any unattached probes.
  7. Hybridised DNA will fluoresce under UV light - or use southern blotting and autoradiography.
56
Q

What are Variable Number Tandem Repeats (VNTRs)?

A

Sequence of bases that repeat next to each other over and over.
e.g. CATCATCATCATCATCAT
They can occur in lots of places in the genome.

The number of repeats differs from person to person. The more closely related you are the more similar your tandem repeats.

57
Q

Describe how genetic finger printing is carried out (6 marks)

A
  • DNA extracted from sample and cut using restriction endonuclease.
  • DNA fragments separated according to length using electrophoresis.
  • DNA made single-stranded.
  • Southern blotting.
  • Apply radioactive probe.
  • Identify probe and therefore tandem repeats using autoradiography.
58
Q

What is a ladder and how is it used in genetic fingerprinting?

A

A DNA ladder is made from DNA fragments of known length to allow you to work out the length of other fragments through comparison.

59
Q

What are the uses of genetic fingerprinting?

A
  • Determining genetic relationships
  • Determining genetic variability within a population
  • Forensic science
  • Medical diagnosis
  • In animal and plant breeding

Biology (17 decks)

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