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Year 1 Semester 1 > Genetics > Flashcards

Genetics Flashcards

1
Q

Give examples of how recombinant DNA technology has helped the food industry

A

-Chymosin
-Golden rice

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2
Q

Give examples of how recombinant DNA technology has helped the pharmaceutical industry

A

-Human insulin
-Human growth hormone
-Blood clotting factor VIII
-Hepatits B Vaccine

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3
Q

What are the three stages of recombinent DNA technology?

A

1 Creation - construction of new combinations of unrelated genes in the test tube.
2 Clone - Amplifying the new DNA many times
3 Using - Expressing a gene to produce a protein.

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4
Q

What does recombinant DNA technology require?

A

-Enzymes to manipulate DNA/RNA
-Vectors which act as a vehicle to carry DNA to host cell
-DNA/RNA nucleotides
-Cells to amplify

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5
Q

What enzymes are required in recombinant DNA technology?

A

-Restriction enzymes
-DNA Ligase
-Taq polymerase (required for PCR)
-Reverse transcriptase (converts RNA to DNA)

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6
Q

What are restriction enzymes?

A

-Rescription enzymes cleave DNA at very specific sequences.
-They are naturally produced by bacteria as a defence mechanism
-Many recognise 4-8 base pair palindromic sequences.

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7
Q

What two types of cleavage patterns do restriction enzymes produce?

A

Symmetrical cleavage (Blunt ends) and Asymmetrical cleavage (Sticky ends)

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8
Q

What is vector DNA?

A

-Made of DNA designed to contain specific components. These include
-a unique restriction site for insertion of new DNA
-An efficient origin of replication
-A gene to allow selection of cells which contain the plasmid (eg Antibiotic resistance)
-Regulatory sequences to allow expression of the inserted gene.

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9
Q

What are the most commonly used vectors?

A

Plasmids.

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10
Q

What are plasmids?

A

-Circular pieces of DNA which occur naturally in some bacteria
-Roughly 2-200 kbp in size
-Replicated independently of bacterial chromosome

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11
Q

What other vectors are available for recombinant DNA Technology?

A

-Bacteriophages (Viruses that infect bacteria)
-Cosmids/Phagemids (Genetically engineered hybrids which replicate as a plasmid but can be packaged as a bacteriophage)

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12
Q

Which bacteria is typically used in recombinant DNA technology?

A

E. Coli

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13
Q

What are the 4 steps in making a clone for recombinant DNA Technology?

A

1 Prepare the insert and vector
2 Ligate the insert into a vector
3 Transform the recombinant DNA into a host
4 Select hosts containing the recombinant DNA

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14
Q

Describe how you create Insert DNA from mRNA for recombinant technology

A

By using reverse transcriptase, converting mRNA into cDNA

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15
Q

Describe how you can ligate an insert into a vector for recombinant technology

A

Once isolated, restriction enzymes are added which create sticky ends on the plasmid and insert. Ligase is then added, binding the insert into the cleaved plasmid.

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16
Q

Describe how you transform the recombinant DNA into a host.

A

The recombinant DNA is mixed with competent cells. Some of these cells take up the plasmid, and they are selectively cultured.

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17
Q

How can we make cells competent for recombinant DNA technology?

A

Heat shock and CaCl, which makes the cell wall porous. Once the plasmid is added the cells are incubated at 37c in order to repair the porous walls.

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18
Q

How do we select the cells that have taken up the plasmids for recombinant DNA technology?

A

Transformed cells are grown on a selective medium (eg containing antibiotics), killing all the cells without a plasmid. However, not all plasmids contain the insert, some will simply religate.

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19
Q

How can we distinguish plasmids with or without an insert?

A

pUC18 plasmids with an insert can be distinguished by insertional inactivation. Insertion of DNA fragment into polylinker disrupts the lacZ gene, inactivating b-galactosidase. They differ in colour (with insert appears white whereas without appears blue)

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20
Q

What checks can be done to check bacteria have taken up the plasmid containing the insert during recombinant DNA technology.

A

-Hybridisation to ssDNA probe complementary to the sequence of interest
-PCR using primers specific for the sequence of interest
-Screen for expression of protein encoded by the sequence of interest.

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21
Q

What can we use recombinant DNA for?

A

-To induce expression of a protein in a host
-Recover the plasmid and manipulate further
-Recover the plasmid and manipulate further.

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22
Q

How do we ensure that the insert is in the correct direction/orientation in the plasmid?

A

Cleaving the insert with 2 enzymes leads to the sequence being ligated in only one possible direction.

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23
Q

What hosts can be used for recombinant DNA technology?

A

-Bacterial cells
-Yeast cells
-Insect cells
-Mammalian cells

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24
Q

Name some advantages for using Bacteria as hosts for recombinant DNA technology

A

+Simple cells
+Short generation time
+Large yields of product
+Low costs

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25
Q

Name some disadvantages for using Bacteria as hosts for recombinant DNA technology

A

-Eukaryotic proteins can fail to fold correctly and lose biological activity.
-Proteins can be toxic to the bacterial cell
-No post-translational modifications.

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26
Q

Name some advantages for using yeast cells as hosts for recombinant DNA technology

A

+Simple unicellular eukaryote
+Resembles mammalian cells
+Grows quickly and cheaply
+Performs post-translational modifications.

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27
Q

Name some disadvantages for using yeast cells as hosts for recombinant DNA technology

A

-Contains proteases, which may degrade some recombinant proteins
-Post-translational modifications may differ from mammalian cells.

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28
Q

Name some advantages and disadvantages for using insect cells as hosts for recombinant DNA technology

A

+High level protein expression
+Correct folding of mammalian proteins
+Post translational modifications
+Cheaper than mammalian cell culture
-Post translational modifications may differ from mammalian cells

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29
Q

Name some advantages for using mammalian cells as hosts for recombinant DNA technology

A

+Best place to produce mammalian proteins
+Correct folding of mammalian proteins
+Has CORRECT post translational modifications.

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30
Q

Name some disadvantages for using mammalian cells as hosts for recombinant DNA technology

A

-Complex cells
-Grow to lower cell densities
-Expensive

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31
Q

What is genetics?

A

The study of inheritance and the manipulation of genetic information in order to
-improve understanding of how an organism works
-Detect and treat diseases
-Exploit organisms for the benefit of humankind and the environment.

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32
Q

What is a wild type in genetics?

A

An unmodified natural isolate of a species

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33
Q

What is a mutant?

A

An organism that differs from the wild type as a result of a specific change(s) in its DNA sequence

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34
Q

What is a mutation?

A

A specific change in the DNA sequence of an organism that differs from the sequence of a wild type, and is heritable.

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35
Q

Give some advantages of using bacteria in genetics.

A

+Bacteria are generally haploid organisms - easier to identify cells with mutations as they have an immediate effect. Higher organisms are usually diploid or even polyploid, meaning that recessive mutations (as most are) won’t be expressed in them
+Same rules as higher organisms - mutations are random and passed onto progeny through vertical gene transfer.

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36
Q

What is gene transfer?

A

Bacteria inherit DNA from other bacteria and viruses in their environment through lateral gene transfer.

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37
Q

What is transformation?

A

The ability of a cell to acquire DNA released into from other cells in the same environment. This can only occur when they are competent (in an appropriate physiological state).

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38
Q

What is the purpose of transformation?

A

To take up environmental DNA in order to increase the cell’s metabolic or functional capability, helping them to compete more effectively in their environment.

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39
Q

Why is transformation important for genetic engineering?

A

Bacteria that do not develop competence naturally (such as E. coli) have to be induced artificially to take up DNA.

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40
Q

What is bacterial conjugation?

A

Conjugation is the transfer of genes from one bacterial cell (donor) to another (recipient) by direct cell-to-cell contact.

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41
Q

In most cases, what is bacterial conjugation mediated by?

A

A conjugative plasmid.

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42
Q

In most cases of bacterial conjugation, what is transferred from the donor to the recipient?

A

Plasmid DNA

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43
Q

Describe plasmid transfer during bacterial conjugation.

A

1 Donor cell attaches to a recipient cell with its pilus, which draws the cells together, and come in contact
2 One strand of plasmid DNA transfers to the recipient
3 The recipient synthesises a complementary strand to become an F+ cell.
4 The donor synthesises a complementary strand, restoring its complete plasmid.

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44
Q

What is transduction in genetics?

A

Gene transfer mediated by a bacteriophage.

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45
Q

Describe Bacteriophage transduction.

A

-Phages occasionally make mistakes when packaging DNA
-It may be filled with either host chromosomal DNA or a mixture of host and its own.
-This may be injected into a new host.
-If the DNA is homologous it can integrate by homologous recombination.

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46
Q

What is the genome used for?

A

The genome is used as a template to replicate itself prior to each round of cell division, and to specify what RNA and protein molecules are required by the cell.

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47
Q

What enzymes are responsible for DNA synthesis?

A

DNA-Dependent DNA polymerases

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48
Q

Describe Chromosome replication in (circular) bacterial chromosomes.

A

-Initiated at a unique site called the origin of replication (OriC)
-Replication proceeds bi-directionally from the origin to the terminus or terC
-This creates two sites of DNA synthesis called replication forks.

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49
Q

How do we calculate the mutation frequency in a sample.

A

Mutation frequency (MF) = number of mutants / sample size

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50
Q

How may we select for mutants?

A

There are three ways in which we can select for mutants.
I) Negative Selection: Selects against the mutant
growing.
II) Enrichment: The use of a negative selection to inhibit growth of mutants and then killing wild type growing cells using an antibiotic.
III) Positive Selection: Uses selective conditions where only the mutants will grow. Typically in the form of resistance to a phage, chemical compound (e.g. antibiotic) or an intermediate metabolic product.

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51
Q

What is genomics?

A

The acquisition, storage, retrieval and analysis of DNA sequence data.

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52
Q

Which strain of E. Coli is used to study genetics, genomics and recombinant technology?

A

Escherichia Coli K12

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53
Q

Describe E. Coli K12

A

-Circular chromosome with 4.6 million base pairs.
-Encodes 4400 proteins or polypeptides
-Replicates bidirectionally from the oriC to the terC, forming 2 replication forks.
-Takes 40 minutes to replicate entire chromosome
-Most genes are present as 1 copy per cell

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54
Q

Give some examples of PCR applications.

A

-Forensics
-Phylogenetics
-Consumer genomics
-Genotyping
-Agricultural biotech
-Cloning
-Gene expression
-Mutagenesis
-Sequencing

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55
Q

Give the components that make up PCR.

A

-Taq Polymerase
-Template DNA
-Deoxynucleoside triphosphates (dNTPs)
-Primers
-Buffers
-Enzyme cofactors (Mg2+)

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56
Q

Describe some key features of Taq polymerase.

A

-Thermostable
-Elongation is always in the 5’ -> 3’ orientation
-Can be hot-started to improve specificity
-Can be high-fidelity (used for proofreading)

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57
Q

What template DNA is used in PCR

A

-gDNA, plasmid DNA, cDNA.
-Starting amounts differ dependent on DNA type (eg 0.1-1ng of plasmid DNA or 5-50 ng of gDNA per 50 microlitres)
-Different polymerases require differing DNA amounts

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58
Q

Give examples of deoxynucleotide triphosphates.

A

dATP, dCTP, dTTP, dGTP

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59
Q

Why are buffers required for PCR?

A

-They stabilise pH
-Contain KCl (K+ promotes primer annealing)
-Contains cofactors that boost polymerase (Mg2+) by enabling incorportation of dNTPs during polymerisation

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60
Q

Describe the primers used in PCR.

A

-Single stranded
~20 bases (max 40)
-Always provided in 5’->3’ orientation
-Complementary to the template and allows polymerase activity

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61
Q

Which way do forward primers bind in PCR?

A

FP binds to the 3’->5’ complementary (antisense/minus) strand

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62
Q

Which way do reverse primers bind in PCR?

A

RP binds to the 5’->3’ coding (sense or plus) strand

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63
Q

Describe the features we incorporate into primers when designed.

A

-G/C clamp
-No complementary regions between/within primers
-GC content 40-60%
-Melting temperature (Tm around 65C and both within 5C)
-Avoid primer dimers (hairpin, self or cross)

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64
Q

Describe how you find the melting temperature in a primer.

A

2(A+T) + 4(G+C) = Tm

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65
Q

Why do we have controls in PCR

A

-Tests for specificity of primers
-Negative control - no DNA, no primers
-Often include a positive control

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66
Q

Give the steps in PCR

A

1 Denature - Heat to break hydrogen bonds (usually 95C)
2 Anneal - Generally a temp 5C below Tm, where bidning to complementary sequence happens
3 Elongation - Taq polymerase forms the bonds between dNTPs (at ~72C)
4 Amplification - This process is repeated for many many cycles

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67
Q

What can we use to visualise/analyse the products of PCR?

A

Agarose gel electrophoresis

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68
Q

What is RT-PCR used for?

(Reverse transcription)

A

-For amplifying RNA regions
-RNA reverse transcibed into cDNA using reverse transcriptase
-Then perform PCR
-Often used for gene expression analysis

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69
Q

What is qPCR?

(quantitative PCR)

A

-Same steps as PCR
-With fluorescent labelling to measure amplicons
-PCR machine contains sensors for measuring fluoresence
-Determines the gene copy numbers

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70
Q

What is a model organism? (Genetics)

A

A well established experimental biological system

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71
Q

What are the characteristics of a model organism?

A

-Rapid rate of development
-Easily manipulated (genetically)
-Short life span
-Readily available
-Large numbers offspring per generation

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72
Q

Describe E. Coli as a genetic model organism.

A

-Possibly the simplest
-Gram negative rod shaped bacterium
-Very easy to grow with a rapid generation time (20-30 minutes)
-Genome of MG1655 strain sequenced
-Very easy to genetically manipulate and transform
-HOWEVER PROKARYOTIC :(

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73
Q

Give some examples of eukaryotic models for genetic analysis.

A

-Yeast
-Fruit flies
-Worm
-Zebra fish
-Mice

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74
Q

What is a Homologue (Gene)?

A

A gene related to another gene by descent from a common ancestral DNA sequence.

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75
Q

What is an orthologue (Gene)?

A

Genes in different species that evolved from a common ancestral gene. Normally retain same/similar function.

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76
Q

What is a paralogue (gene)?

A

Paralogues are genes generated by a duplication event (eg Human alpha and beta haemoglobin genes)

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77
Q

What is gene knockout?

A

Gene sequences are completely or partially removed and gene expression is completely eliminated.

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78
Q

What is gene knockdown?

A

Techniques that reduce/interfere with the expression (eg translation) of a gene (eg RNA interference)

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79
Q

Describe yeast as a model organism.

A

-Unicellular eukaryotics
-Linear chromosomes in a nucelus
-Divide by budding or fission (depending on species)
-Budding yeast or Fission yeast.

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80
Q

Describe budding yeast as a genetic model.

A

-Small size and simple growth and storage conditions
-Rapid growth rate (80mins/gen)
-Can exist as diploid or haploid cells
-12.8 Mbp genome
~6000 genes
-Have a sexual cycle (enabling genetic crosses)
-Easily transformable with plasmids
-Gene knockouts and knockins easy
-Large mutant collections

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81
Q

Describe fission yeast as a genetic model.

A

-Fission yeast (splits to divide)
~13 Mbp with ~5000 genes
-Has all the same research advantages as budding yeast
-But highly evolutionarily divergent

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82
Q

Describe fruit flies as a genetic model.

A

-Small (3mm) and large numbers can be maintained
-Short lifespan (~2 weeks, producing 100 eggs per day)
-Genome 165 Mbp, ~14000 genes
-Easy to cross genetics
-Lots of mutants
-Mature larvae produce giant polytene chromosomes allowing genetic mapping
-Transformable using P element transposon
-Possible to do tissue specific knockdowns or deletions

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83
Q

What are transposons?

A

Jumping genes - DNA sequences that move from one location on the genome to another

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84
Q

What is a disease model (genetics)?

A

A mutant model organism that mimics the phenotypes/features observed in a human disease.

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85
Q

Give an example of Drosophila (fruit fly) disease models.

A

Spinal muscular atrophy
-Caused by mutations in human SMN genes.
-Drosophila strains carrying mutations in its orthologous SMN genes habve phenotypes analogous to the human pathology.

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86
Q

Describe C. Elegans as a genetic model.

A

-Small (1mm) free living
-Transparent, allowing for easy observation and manipulation
-Feeds on bacteria, meaning it can be cheaply maintained, cultivated and transformed (consuming bacterial plasmids)
-Short lifespan (2-3 weeks)
-Two sexes allowing for genetic crossing
-Can produce about 300 offspring
-Genome 97Mbp ~20000 genes (40% have human orthologues)
-Genes can be knocked down using RNA interference

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87
Q

Describe RNA interference.

A

1 dsRNAs complementary to the gene of interest are introduced
2 dsRNAs are processed to short interfering RNAs
3 siRNAs prevent expression of gene of interest.

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88
Q

Describe zebrafish as a genetic model.

A

-Vertebrate
-Lay 200 eggs per week and sexually mature at 3-4 months
-Transparent embryos (can see changes during development)
-1.7 Gbp genome - 25 chromsomes
-Sturdy embryos that can be injected
-Possible to make mutants by random mutagenesis
-Manipulating genomic DNA is now becoming available
-Knockdown of expression of specific genes is possible using morpholinos.

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89
Q

What are morpholinos?

A

Small oligomers of synthetic nucleotide analogues that block gene expression.

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90
Q

Describe Mice as a genetic model.

A

-Model most closely related to humans
-25000 genes with 2.6 Gbp
-13000 orthologous genes aligned for humans
-2 month breeding cycle
-Manipulation of Embryonic SCs allows production of transgenic mice (containing additional foreign DNA in every cell)

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91
Q

Give examples of Mouse disease models.

A

-Cancers
-Blindness
-Obesity
-Diabetes
-Drug addiction
-Alcoholism
-Aggression
-Anxiety

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92
Q

What percentage of the human genome are made up of protein coding genes?

A

~2%

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93
Q

Give an example of a dye used to stain the chromosome during a karyotype?

A

GIEMSA

94
Q

What is a chromatid?

A

During mitosis chromosomes become highly condensed and thus visible, these are known as chromatids. The contain centromeres and Telomeres.

95
Q

Do chromosomes separate or mix together in the nucleus of a cell?

A

Chromosomes that are not undergoing division are decondensed and occupy a distinct “territory” within the nucleus.

96
Q

What are centromeres?

A

-Regions where sister chromatids are held together.
-Centromeres are the assembly site for a protein complex called the KINETOCHORE

97
Q

Give examples of different types of chromosomes, based upon centromere position.

A

Metacentric, Submetacentric, Arcocentric, and Telocentric

98
Q

What are telomeres?

A

-Specialised regions at the end of chromosomes.
-They are composed of hundreds of repeated motif (5’TTAGGG3’)

99
Q

What are the two functions of telomeres?

A

-They allow the cell to distinguish a real chromosome end from an unnatural end caused by a chromosome break.
-They solve the problems that cells have replicating the ends of linear chromosomes (END REPLICATION PROBLEM)

100
Q

GIve the properties of Telomerase and Telomeres.

A

-We are born with full-length telomeres due to the activity of telomerase during development.
-In nearly all somatic cells telomerase is turned off
-Telomeres therefore shorten during each cell-division.
-Eventually our cells recieve defective chromosomes since their ends are damaged anbd can no longer survive. (REPLICATIVE CELL SENESCENCE)

101
Q

Describe Chromatin

A

-Genomic DNA in Eurkaryotes is associated with histones
-DNA is wrapped twice around an octamer of histones to form a nucleosome
-Arrays of nucleosomes are further compacted into 30nm chromatin fibre

102
Q

Give types of Chromatin

A

Euchromatin and Heterochromatin

103
Q

What is euchromatin?

A

Relatively uncondensed associated with active (expressed) genes

104
Q

What is heterochromatin?

A

Condensed, associated with repetitve gene poor regions that are inactive (silenced)

105
Q

Give some examples of unusual chromosome types

A

-Minichromosomes
-B Chromosomes
-Holocentric chromosomes
-Polytene chromosomes

106
Q

What is the kinetochore?

A

A protein structure located at the centromere that serves as an attachment point for the mitotic spindles

107
Q

What are spindle fibres?

A

Formed from microtubules that run between the poles of the cell creating an axis for the separation of chromosomes

108
Q

What is the centriole?

A

A cytoplasmic organelle composed of 9 groups of microtubules that serve as the foci for the generation of mitotic spindle fibres

109
Q

What is the centrosome?

A

A region of the cytoplasm containing a pair of centrioles

110
Q

What are chiasmata?

A

-A physical connection between non-sister chromatids.
-Results in genetic exchange between members of each pair of homologous chromosomes
-Creating chromosomes which are mosaics of the maternal and paternal chromosome

111
Q

When does the formation of Chiasmata occur?

A

During prophase 1

112
Q

What are the 5 stages of prophase 1?

A

-Leptonema
-Zygonema
-Pachynema
-Diplonema
-Diakinesis

113
Q

Describe what happens in each stage of Prophase 1.

A

Leptonema - Duplicated chromosomes start to condense
Zygonema - Synapsis begins
Pachynema - Synapsis complete, crossing over occurs
Diplonema - Synaptonemal complex disappearing and chiasma are visible
Diakinesis - Bivalent ready for metaphase

114
Q

What is the synaptonemal complex?

A

A nucleoprotein “zipper” that forms between the paired homologous chromosomes.

115
Q

Are there many eukaryotes that reproduce asexually?

A

There are very few that have mostly evolved very recently - suggesting a high extinction rate.

116
Q

What is the beneefit of sexual reproduction?

A

-Results in the production of recombinant genotypes
-Making the population better able to deal with changes in environment

117
Q

Give an example of a study that supports the benefit of sexual reproduction.

A

-Goddard et al. (2005)
-Sex offered no benefit in the benign environment (meaning asexual strain grew faster), but in the harsher enviroment sexual populations adapted more rapidly and survived better than the asexual population.

118
Q

Describe the protenor method of sex determination.

A

The presence or absence of an X cromosome in the Male gamete determines sex.
-XX = Female.
-XO = Male.

119
Q

Describe the Lygaeus method of sex determination.

A

The presence of a Y chromosome in the Male gamete determines sex.
-XY = Male
-XX = Female

120
Q

What is the difference between heterogametic and homogametic?

A

Heterogametic sexes can either produce X, Y or O gametes, whereas homogametic sexes can only produce X gametes.

121
Q

Give some features of the Y chromosome.

A

-PARs = pseudoautosomal regions
-MSY = male specific region of the Y
-SRY = Sex determining region Y

122
Q

What are PARs/pseudoautosomal regions and MSY/Male specific regions of Y?

A

PARs are Regions that share homology with the X chromosome. These regions synapse and recombine with the X chromosome during meiosis.
MSYs are regions that do not synapse with the X chromosome.

123
Q

What is SRY/Sex determining region Y?

A

A region that produces Testis Determining Factor (TDF) which triggers undifferentiated gonadal tissue of the embryo to form testes.

124
Q

Is there any alternatives to chromosomal sex determination?

A

-In some reptilian species sex determination is achieved according to incubation temperature of eggs - Temperature dependent sex determination
-Temp affects the activity of enzymes and inhibitors controlling the production of steroid hormones such as estrogen.

125
Q

What does Lyonisation/The Lyon hypothesis suggest?

A

-One X chromosome in the female is inactivated
-Inactivation is random at an early point in development
-Once inactivated all progeny cells have the same X-chromsomes inactivated
-Females are mosaics for all X-linked genes, some cells express paternal info, some maternal.

126
Q

Describe the mechanism for the inactivation of the X chromosomes

A

-Inactivation is initiated from a site called XIC (X-inactivation centre)
-Key products include two non-coding RNA (Xist and Tsix).
-Xist progressively coats one X chromsome spreading outwards from XIC
-Leads to the packaging of one X chromosome into a very dense compacted Heterochromatin
-(However 15% of genes escape inactivation).

126
Q

How are bacterial genes organised?

A

-Clustered genes are often transcribed as a single molecule of mRNA
-this mRNA is polycistronic
-Co-transcribed genes often encode proteins involved in the same process/biochemical pathway.

127
Q

Are eukaryotic genes monocistronic or polycistronic?

A

-Each gene has a single transcription unit (monocistronic)
-Since each gene has its own promoter, coordination of gene expression in eukaryotes is different to bacteria

128
Q

What do eukaryotic mRNAs contain that aid in translation.

A

-A Cap (5’) and PolyA tail (3’)

129
Q

What are transcription promoters?

A

Region of DNA upstream of a gene that contains specific nucleotide sequences with which transcription factors can associate. These factors then recruit RNA Polymerase.

130
Q

Give some key features of a prokaryotic transcription promoter?

A

-Conserved sequences upstream (-35 and -10) of the start site
-The conserved sequenves are recognised by a σ(sigma) factor.
-This positions the polymerase allowing initiation of transcription
-RNA Pol + σ factor = holoenzyme.

131
Q

How many RNA Polymerases do Bacteria have?

A

Only One!

132
Q

How many RNA polymerases are present in eukaryotes and what are their names?

A

3!
-RNA Pol I - Ribosomal RNA
-RNA Pol II - All protein coding genes
-RNA Pol III - tRNA, ssRNA, other small noncoding RNAs

133
Q

Give the key features of RNA Pol II promotors in Eukaryotes.

A

-Promoter comprises various sequences that are binding sites for factors that either stimulate or repress transcription
-Most important is TATA-box which is bound by the transcription factor 2D complex
-TFIID recruits other transcription factors and RNA Pol II
-The 5’ Cap is added while the mRNA is transcribed

134
Q

Describe Eukaryotic transcription terminator regions.

A

-Transcripts end 10-35 nucleotides downstream of a specific signal
-Here the RNA is cut by an endonuclease to release it from the DNA
-And the polyA tail is then added.

135
Q

Describe how Prokaryotes can alter gene expression.

A

-Alternative σ factors that recognise different -35/-10 sequences
-These control sets of coordinately regulated promotors eg heat-shock
-Mutation to a single σ factor affects expression of the set of genes that it regulates

136
Q

Describe how Eukaryotes can alter gene expression.

A

-Many different transcription factors bind sequences in the promotor
-These influence the ability of RNA Pol II to initiate transcription
-This allows any stimuli to regulate each promotor and hence gene

137
Q

What is a gene?

A

A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and or other functional sequence regions.

138
Q

Describe the ribosome.

A

-Ribosome comprises 2 subunits (large and small)
-The small subunit is responsible for reading the mRNA - finding the start of Open reading frames in mRNA and interpreting each codon.
-The large subunit houses the protein synthetic peptidyl transferase centre

139
Q

Describe initiation of bacterial translation.

A

-The Shine-Dalgarno sequence is recognised directly by the small subunit by base pairing
-The large subunit binds to the small subunit and translation then initiates on the downstream AUG
-The Shine-Dalgarno sequence allows independent translation of each ORF in a polycistronic mRNA

140
Q

What sequence initiates translation in eukaryotic organisms.

A

The Kozak consensus sequence.

141
Q

Define the dominant allele.

A

The allele that expresses itself at the expense of an alternate allele; the phenotype expressed in the F1 generation from the cross of two pure lines

142
Q

Define the recessive allele.

A

An allele whose expression is suppressed in the presence of a dominant allele; this phenotype will disappear in the F1 generation from the cross of two pure lines and reappear in the F2 generation.

143
Q

What is the Hardy-Weinberg equation for allele frequency?

A

p + q = 1

144
Q

What is the Hardy-Weinberg equation for genotype frequency?

A

p² + 2pq + q² = 1

145
Q

When does the Hardy-Weinberg equation not apply?

A

When there is
-Gene flow (movement of an individual into an isolated population)
-Genetic drift (small populations leading to interbreeding)
-Nonrandom mating (sexual selection)
-Natural selection (ability to produce more offspring through differing survival or family size)

146
Q

What characterises an autosomal recessive pedigree?

A

-Generally, disease appears in progeny of unaffected parents
-Horizontal degree pattern
-Affected progeny include both males and females

147
Q

What characterises an autosomal dominant pedigree?

A

-Appear in each generation of a pedigree (vertical degree pattern)
-Usually (unless affected individual homozygous) 50% of offspring affected
-Affected fathers and mothers transmit the phenotype to both sons and daughters

148
Q

What is a reciprocal cross?

A

When the genotypes of parents are swapped, in order to investigate whether a certain trait is X-linked.

149
Q

What is incomplete dominance?

A

A form of Gene interaction in which both alleles of a gene at a locus are partially expressed, often resulting in an intermediate phenotype (eg white flower + red flower = pink flower)

150
Q

What is codominance?

A

When two alleles for a trait are equally expressed with neither being recessive or dominant (eg blood groups - A + B = AB)

151
Q

What is pleiotropy?

A

Where a single gene affects multiple characteristics.

152
Q

What is epistasis?

A

Where one gene affects the expression of another gene.

153
Q

What is penetrance in genetics?

A

-Penetrance describes how many members of a population with a particular genotype show the expected phenotype.
-Penetrance can be complete (100%) or incomplete. If 15% of individuals with a particular mutation appear wild-type, the penetrance is said to be 85%

154
Q

What is expressivity in genetics?

A

Variable expressivity refers to the range of signs and
symptoms that can occur in different people with the same genetic condition

155
Q

What is a complementation group?

A

A set of mutations mapping to the same chromosomal locus that fail to complement each other when crossed (they produce a mutant phenotype when combined).
-They can only be done with recessive alleles
-With proteins with only a single function

156
Q

How is recombination frequency calculated?

A

Recombination frequency (centimorgans %) = (number of recombinents/total) x 100

157
Q

What are syntenic genes?

A

Syntenic genes are those grouped in the same way on the chromosomes of multiple species.

158
Q

In comparitive genome analysis, what do syntenic blocks mean?

A

regions containing homologous genes.

159
Q

Is p or q the long arm of a chromosome?

A

q is the long arm.

160
Q

Is p or q the short arm of a chromosome?

A

p is the short arm

161
Q

What is reciprocal translocation?

A

Where 2 non-homologous chromosomes break and exchange fragments.

162
Q

What is centric fusion of chromosomes?

A

Where 2 telocentric chromosomes fuse to generate 1 new chromosome.

163
Q

Describe Inversion in genome evolution.

A

-Occurs when a section of DNA breaks away and reattaches in the reverse order.
-Can be paracentric (within 1 arm) or pericentric (within both arms)

164
Q

Describe Robertsonian translocation

A

When the short arms of two arcocentric chromosomes are lost.

165
Q

Describe sister chromatid exchange.

A

Two pairs of sister chromatids line up during meiosis and a repetitive region of one chromatid does not line up exactly with corresponding regions. Strand breaks and exchange, leading to expanding chromatids.

166
Q

Describe de novo generation of genes.

A

Transcription at any part of the genome can potentially lead to a protein being made, which if advantageous or neutral may be retained and can evolve over time into a new gene.

167
Q

What is a multigene family?

A

A group of genes that have descended from a common ancestral gene and therefore have similar functions and DNA sequences.

168
Q

What causes the formation of multigene families?

A

Arise after duplication events, followed by mutation allowing alterations in expression/function.

169
Q

What are Variable Number Tandem Repeats.

A

Our genomes have at many places repeated sequences organised as sequential (tandem repeats). These vary between individuals, meaning that we can use these to identify different individuals.

170
Q

Give the two types of microsatellites.

A

Simple sequence repeats (SSRs) and Short tandem repeats (STRs)

171
Q

Describe Microsatellites

A

-Short repeating units of ~5 nts or less
-Repeated usually less than 100x
-Repeat number frequently varies between individuals
-Found throughout the genome (every few 1000 bp)

172
Q

Describe Minisatellites

A

-Repetitive (generally GC-rich), variant repeats of 10-100 bases.
-Variants are interspersed
-In humans, 90% of minisatellites at the sub -telomeric region of chromosomes.

173
Q

What are Single nucleotide polymorphisms.

A

-Single base differences (called SNPs)
-Can be very informative when looking for association across the genome with particular phenotypes
-SNPs are approximately 1 every 300 nts
-Some base changes produce new sites for restriction endonucleases creating different sizes of fragments on southern blot, creating
RESTRICTION FRAGMENT LENGTH POLYMORPHISMS

174
Q

What are CpG islands?

A

Regions of DNA highly enriched in CgP sites.
-Frequently associated with 5’ region (promoters) of genes (around 70% in humans).

175
Q

What is a haplotype?

A

A set of linked polymorphic markers.

176
Q

What can an SNP map of the human genome be useful for?

A

-Locating genes that might be associated with particular phenotypes
-Diagnosing potential (future) problems/phenotypes

177
Q

Give examples of elaborate structures made from RNA folding.

A

-Three nucleotide bulge
-Four stem junctions
-Hairpin loop
-Pseudoknot

178
Q

What is a Progenote?

A

An organism still in the process of evolving the relationship between genotype and phenotype

179
Q

Can rRNA act as a catalyst?

A

It can catalyse protein synthesis

180
Q

How old is prokaryotic life?

A

3.75 Billion Years

181
Q

How old is Eukaryotic life?

A

At least 1.6 Billions years old

182
Q

How can we generate evolutionary trees from genomes?

A

-Make an alignment of the gene or protein sequences
-Measure the similarity between sequences
-Convert simillarity to evolution distance estimates using a mathematical model
-Draw a tree that best fits the pair-wise distance estimates between sequences

183
Q

Give an example of a complex chronometer.

A

Small subunit ribosomal rRNA

184
Q

What is Mitochondrial Hsp70 required for?

A

-Plays a role in protein import into the mitochondria and assembling Fe-S clusters

185
Q

What are the two theories for origin of modern humans?

A

-The multiregional model
-The out of africa hypothesis

186
Q

What is the multiregional model for the origin of modern humans?

A

The Multiregional Model proposes that modern human (Homo sapiens) populations arose independently in different parts of the world from isolated populations of Homo erectus

187
Q

What is the Out of Africa hypothesis for the origin of modern humans?

A

The Out of Africa hypothesis proposes that modern humans originated in Africa, members of this species moving into the rest of the old world displacing the descendants of Homo erectus that they encountered.

188
Q

What is developmental biology?

A

The study of the process by which organisms grow and develop, focusing on growth, differentiation and morphogenesis.

189
Q

When do we focus on developmental biology in mammals?

A

Between fertilisartion and Birth

190
Q

When is the embryonic stage of pregnancy?

A

Up to 8 weeks

191
Q

When is the fetal stage of pregnancy?

A

Between 8 weeks and term

192
Q

What are the three approaches to studying development?

A

-Anatomical
-Physical
-Genetic

193
Q

What are human organoids?

A

Self-organising 3D cell cultures, derived from pluripotent stemcells

194
Q

What do most cancer cells have mutated?

A

Changed/non-functional G1 checkpoint

195
Q

What tools are available to study genetics?

A

-Morpholinos
-Chemical mutagenesis
-Transgenesis
-Single gene knockouts/knockins
-Conditional gene knockouts
-CRISPR

196
Q

What is Morphogenesis?

A

-Biological process whereby an organism or structure begins to develop 3D form

197
Q

What is Axis formation?

A

-The establishment of body plan, the map of an organism

198
Q

What are the three axes of an organism.

A

-Antero-Posterior Axis (Head-Tail)
-Dorso-Ventral Axis (Back-Belly)
-Left Right Axis

199
Q

What controls the patterning of an embryo, and how?

A

Growth Factors (Morphogens), which activate different genes at different concentrations

200
Q

Describe the Anterior visceral endoderm (AVE).

A

-The first signalling centre to appear
-Patterns only the anterior part of the embryo
-The node patterns the whole embryo, working cooperatively with the AVE at the anterior end of the embryo

201
Q

Describe the Left-Right axis signalling pathway.

A

-Initiated at the node
-Release of secreted morphogens (shh,RA,FGF) breaks symmetry
-Results in a specific signalling pathway only on the left side
-Nodal activates Pitx2 which regulates downstream gene expression

202
Q

What morphogens pattern the Anterior-Posterior axis?

A

-Wnt signals specify the anterior region
-RA patterns the midbrain, hindbrain and trunk
-FGF gradient patterns the caudal region
-This results in the expression of specific homeobox containing genes in different regions of the embryo

203
Q

Describe Dorsal-Ventral patterning.

A

-Neural tube is patterned (BMP from dorsal region, Shh from ventral region)
-Opposing gradients of Shh and BMP specify neuronal subtypes
-Activates expression of homeobox genes

204
Q

Describe congenital malformations.

A

-Present at birth
-Usually occur during embryogenesis
-Result from disruption of normal development and occur due to genes or environment.

205
Q

Give some genetic causes of congenital malformations.

A

-Chromosomal defects
-Syndromes
-Single genes
-Multigene interactions

206
Q

Give some environmental causes of congenital malformations.

A

-Radiation
-Maternal diabetes
-Fever
-Prescription drugs
-Recreational drugs
-Pollutants
-Dietary deficiencies

207
Q

What are the key methods for anatomical approach of studying congenital malformations?

A

-Gross morphology (Dissection)
-Histology
-Embryos/tissues dehydrates
-Embedded in paraffin wax
-Thin slices cut
-Different tissues/cell tyoes visualised

208
Q

What are the key methods for physical approach of studying congenital malformations?

A

-Removal of part of the embryo and looking at its consequences
-Replacing one part of an embryo with another
-Using drugs to interfere with a developmental process

209
Q

What are the key methods for genetic approach of studying congenital malformations.

A

-Visualisation of gene/protein expression
-Transcriptomic sequencing
-Measurement of levels of gene/protein expressions (qPCR, western blotting)
-Disruption of gene function (total or conditional knockout)
-Ectopic gene expression

210
Q

What is the difference between total and conditonal knockout?

A

Disruption of gene function in either all cells or a certain cell type of choice

211
Q

What methods are there for analysing gene expression?

A

-In situ hybridisation (mRNA)
-Immunohistochemistry (protein)
-Linkage of gene regulatory elements to a reporter gene (transgenesis)

212
Q

What is gastrulation?

A

-The process where 3 germ layers are formed
-Occuring early in development and is key process in formation of the embryo, involving cell signalling

213
Q

What 3 specialised cell types are formed during gastrulation?

A

-Ectoderm (eg skin, neurones, pigments)
-Mesoderm (cardiac, skeletomuscle, RBC, smooth muscle)
-Endoderm (Alveolar, Thyroid, Pancreatic)

214
Q

Give an example of how developmental biology has helped us to understand congenital disease

A

Gross morphology of Lp mouse showed that the neural tube closure isn’t initiated, giving us the cause for Neural tube defects which affect ~2/1000 live births
-Allows for genetic counselling, and therapies including Folic acid.

215
Q

What is the difference between Group I and Group II introns?

A

Group I introns are self-splicing introns that require exogenous guanosine or a guanosine nucleotide for splicing. Group II introns are also self splicing but they use a different method.

216
Q

What syndrome occurs due to trisomy 13?

A

Patau Syndrome

217
Q

What is anhidrotic ecodermal dysplasia?

A

X-linked mutation which causes absence of sweat glands males carrying mutant allele (d) d/Y gene have no sweat glands. Heterozygous female. D/d has mosiac of D and sectors across the body.

218
Q

What type of condition would result in affected males passing the disease to all of their daughters but none of their sons?

A

X-linked dominant disorder

219
Q

What is meant by the term gene flow?

A

The movement of an individual into an isolated population

220
Q

What does SELEX stand for and what is the correct order of the steps involved?

A

Systematic Evolution of Ligands by EXponential enrichment
1. Select a large library of random sequences
2. Selection of sequences with high activity or binding
3. Separate RNA with desired properties
4. Amplify the desired RNA
5. Create mutations of the selected RNA
6. Repeat

221
Q

What are transitional base-pair mutations?

A

Transitional base-pair mutations is the interchange of two purines or two pyrimidines. In other words, the complementary bases G and T swap positions. In some cases, this does not alter the amino acid product{1}. However, tranversions are the interchange of a purine for a pyrimidine and vice versa which has a higher change in changing the transcripts sequence, increasing the risk of a mis-sense or non-sense mutation.

222
Q

Neural Tube Defects are multigene abnormalities in neurulation. Mice and flies were used to study the effect of genes on the presence of the abnormalities, what were found to be their respective homologues?

A

Mice: Lp
Flies: Vangl2

223
Q

True or false:
A paracentric inversion is an inversion that occurs only within one arm of a chromosome.

A

TRUE

224
Q

In eukaryotes, which of the following steps correctly describes the first action of the ribosome in the initiation of translation?

A

The small subunit binds to the CAP, and moves to the first AUG sequence

225
Q

Yeast species can be used as models to study human genetic disorders. The human genes WRN/ BLM are associated with Werner and Blooms syndrome, what is the species of yeast with its associated homologue(s)?

A

Species: Saccharomyces cerevisiae
Homologue: SGS1

226
Q

What is true about meiosis in females and their gametes?

A

Meiosis II completes only after fertilisation

227
Q

What is G-banding?

A

Wild proteolysis followed by Giemsa (dark band A-T rich)

228
Q

What is exon shuffling?

A

Proteins composed of functional domains, and some exons, correspond to discrete domains. Analysis of extent genes reveals evidence for these acting as modules, and moving around the genome to a new location, and or being duplicated in the content of single genes.

229
Q

What is the name of the Small Subunit (SSU) ribosomal (r)RNA in eukaryotes

A

18S SSU rRNA

230
Q

Where does Wnt pattern?

A

Anterior

231
Q

How does the chromosome structure protect the cell against cancer?

A

The cell no longer replicates and initiates a DNA damage response when the telomeres become so short that the chromosomes become damaged. This replicative cell senescence means that the cell will not replicate with damaged chromosomes, the damaged cell will undergo apoptosis and the cell will be protected against cancer.

Year 1 Semester 1 (4 decks)

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