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BIOL 113 - Genetics > Week 14 > Flashcards

Week 14 Flashcards

1
Q

What are the advantages of bacteria for genetic study?

A
  • Easily cultured (can be grown in many different types of cultures)
  • Short generation time: 20-30mins
  • Haploid (mutations can be identified immediately, it won’t be masked)
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2
Q

Features of E. coli nucleoid?

A
  • Chromosome is a single double stranded circular DNA molecule
  • 4.6 million base pairs in length, and contains ~ 4500 genes.​
  • DNA is compacted by coiling up in a structure (called the nucleoid), which occupies a large fraction of the cell volume.​

​

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3
Q

What is a bacteriophage?

A

Virus that infects bacteria; their structure and function is diverse

Types include: T7, Lambda, T5, fd, T4

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4
Q

What are the two types of bacteriophage life cycles? Briefly outline these two cycles?

A

Lytic (multiply + lyse releasing progeny bacteriophage particles)

Temperate/lysogenic (integrate into bacterial chromosome and remain dormant, replicate with bacterial DNA)

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5
Q

Genes can be transferred between bacteria and genetic recombination produces new bacterial strains. How?

A
  • Mutations create new alleles
  • Recombination = new combinations of alleles
  • Gene transfer and recombination occurs through: transformation, transduction, conjugation
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6
Q

Define recombination?

A

The combining of DNA from two individuals into a single genome

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7
Q

Gene transfer in bacteria: transformation

A

Uptake of naked DNA from one bacteriophage to another bacteriophage

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8
Q

Gene transfer in bacteria: transduction?
What are the two types?

A

Transfer of bacterial genes from one bacteria to another

Two types:
- Generalised (only virulent phage)
- Specialised (only temperate phage)

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9
Q

Gene transfer in bacteria: conjugation?

A

The ability to form sex pili and to transfer DNA by conjugation is determined by a plasmid - F (fertility) factor

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10
Q

What is the role of the F Factor in conjugation?

A
  • F Factor replicates with bacterial chromosome
  • One end of the DNA molecule passes through the cytoplasmic bridge into recipient cell (exconjugant) where it circularises.
  • Donor keeps copy of F Factor
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11
Q

How do individual bacteria adapt to their environment?

A

Genes coding for proteins required all the time by bacterial cell = constitutively expressed​

Other genes are only active (expressed) when they are required = regulated genes

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12
Q

Gene expression in bacteria is controlled at what level?

A

Level of initiation of transcription
(beginning when RNA polymerase binds to a promoter)

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13
Q

Tryptophan biosynthesis is regulated by what?

A

Regulated synthesis of repressible enzymes

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14
Q

Tryptophan biosynthesis negative regulation?

A

Binding of repressor/tryptophan to operator blocks transcription

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14
Q

Control of lactose metabolism is regulated by…

When lactose is absent versus present?

A

synthesis of inducible enzymes

Absent: repressor active, operon off
Present: repressor inactive, operon on

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15
Q

How does negative regulation affect gene expression in bacteria: eg in tryptophan & lactose?

A
  • trp operon, expression is off when tryptophan binds to repressor which then binds to the operator. ​
  • lac operon, expression is off in the absence of lactose when the repressor binds to the operator.​
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16
Q

How does positive regulation affect gene expression in bacteria?

A

binding of a molecule to the operator turns on gene expression.​

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17
Q

Positive regulation of gene expression, dependent on the cAMP receptor protein level?

A

Lactose present, glucose scarce so cAMP = high. Abundant lac mRNA synthesis occurs.

Lactose present, glucose abundance so cAMP = low. Little lac mRNA synthesis occurs.

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18
Q

Stage one of the lytic life cycle of a bacteriophage? (use T4 as the example phage)

A

The T4 phage uses its tail fibres to stick to specific receptor sites on the outer surface of an E. coli cell.

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19
Q

Stage two of the lytic life cycle of a bacteriophage? (use T4 as the example phage)

A

The sheath of the tail contracts, thrusting a hollow core through the wall and membrane of the cell. The phage injects its DNA into the cell.

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20
Q

Stage three of the lytic life cycle of a bacteriophage? (use T4 as the example phage)

A

The empty capsid of the phage is left as a “ghost” outside the cell. The cells DNA is hydrolysed

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21
Q

Stage four of the lytic life cycle of a bacteriophage? (use T4 as the example phage)

A

The cell’s metabolic machinery, directed by phage DNA, produces phage proteins, and nucleotides from the cell’s degraded DNA are used to make copies of the phage gnomes.

The phage parts come together. Three separate sets of proteins assemble to form phage heads, tails and tail fibres.

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22
Q

Stage five of the lytic life cycle of a bacteriophage? (use T4 as the example phage)

A

The phage then directs production of lysozyme, an enzyme that digests the bacterial cell wall.

With a damaged wall, osmosis causes the cell to swell and finally burst, releasing 100-200 phage particles

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23
Q

Stage one of the temperate/lysogenic life cycle of a bacteriophage?

A

Phage DNA circularises,

Phage DNA integrates into the bacterial chromosome becoming a prophage.

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24
Stage two of the temperate/lysogenic life cycle of a bacteriophage?
The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells. Many divisions produce a colony of bacteria infected with prophage
25
Stage three of the temperate/lysogenic life cycle of a bacteriophage?
Occasionally, a prophage exits the bacterial chromosome initiating a lytic cycle.
26
What is the generalised type of transduction? (5 stages)
1. Phage infects bacterial cell 2. Host DNA is hydrolysed into pieces and phage DNA/proteins made 3. Occasionally a bacterial DNA fragment is packaged in a phage capsid 4. Transduction phages infect new host cells, where recombination (crossing over) can occur 5. Recombinants have genotypes different from either the donor or recipient.
27
What is the specialised type of transduction? (5 stages)
1. Bacterial cell has prophage integrated between genes. 2. Occasionally, prophage DNA exits incorrectly, taking adjoining bacterial DNA with it 3. Phage particles carry bacterialDNA along with phage DNA 4. Transducing phages infect new host cells where recombination (Crossing over) can occur 5. The recombinants have genotypes different from either the donor or recipient
28
What occurs in conjugation after the F factor male is converted into an Hfr male by integration of the F plasmid into the chromosome?
- Conjugation between a Hfr and F- bacterium, - Recombination between the transferred fragment and the F- chromosome
29
In Eukaryotes, linear DNA is organised into what?
Chromatin
30
Why are eukaryotic genomes generally so large?
1. number of genes (more genes, reflecting greater complexity of the organisms) 2. amount of non-coding DNA (most DNA doesn't encode protein or RNA, most consist of: non-coding sequences including gene regulatory sequences (eg promoters), introns, sequences of unknown function)
31
What is the promotor, exon and intron part of DNA causing eukaryotic genes to be so large?
Promoter: the part of the gene that controls its transcription​ Exon: transcribed sequence that is represented in the final mRNA​ Intron: intervening sequence in the transcribed region that is not represented in the final mRNA
32
What are the two types of repetitive sequences that make up a lot of the genome in a eukaryote?
1. Interspersed repetitive DNA 2. Tandemly repetitive (satellite) DNA
33
What is Interspersed repetitive DNA sequences in eukaryotes?
- Repeated units scattered throughout the genome - Single unit 100-10,000 bp - Copies not necessarily identical, but closely related - Make up 25-40% of most mammalian genomes - eg Alu elements make p 5% of mammalian genome
34
How are interspersed repeats and tandemly repetitive (satellite) DNA in human chromosomes detected?
By the use of fluorescent tags
35
What is Tandemly repetitive (satellite) DNA sequences in eukaryotes?
- Can be broadly classified according to the length of a single repetitive region - Most located at telomeres and centromeres (structural role) - Some genetic disorders are caused by abnormally long stretches of repetitive sequences eg Huntington's
36
What are the different classifications of Tandemly repetitive (satellite) DNA sequences in eukaryotes according to length of a single repetitive region?
-Regular satellite DNA: 100,000-10 million bp per site​ - Minisatellite DNA: 100-100,000 bp per site​ - Microsatellite DNA: 10-100 bp per site​
37
Chromatin structure in eukaryotes?
Chromosomes are composed of chromatin (protein + DNA) Chromatin is an intricate form of packaging for DNA (10,000-fold compaction)
38
Why chromatin?
DNA in a cell must be packed in an organized manner to be accessible for transcription and replication​; involves association with histones and the formation of chromatin​
39
What is the difference with heterochromatin and euchromatin in eukaryotes?
Heterochromatin: highly condensed during interphase, not actively transcribed​ Euchromatin: less condensed during interphase, able to be transcribed​
40
What does packaging of chromosomes in eukaryotes begin with?
the nucleosome (the basic unit of chromatin) 1. Histones: proteins with positively charged amino acids that bind to the negatively charged DNA​ (Play a key role in chromatin structure​)
41
Higher orders of packaging chromosomes involves what?
The 30nm chromatin fibre During interphase, most of the chromosome is in the form of euchromatin, where the 30nm chromatin fibre is looped around.
42
During meiosis and mitosis the chromatin folds further (condenses), forming what?
Highly condensed chromatin also occurs during interphase in some regions of the chromosome forming heterochromatin
42
During what process in multicellular eukaryotes, is there long-term control of gene expression additional to internal and external environmental response?
Cellular differentiation When a zygote is given its 'cellular roles' (There are over 200 different cell types in the human body. Each cell expresses only 3-5% of its 20,000 genes at any given time)
43
Gene expression regulation can occur at any step from gene to protein including?
1. DNA unpacking 2. Transcriptional control 3. RNA processing control 4. RNA transport/localisation control 5. mRNA degradation control 6. Translation control 7. protein activity control
44
Coarse adjustment of gene expression by chemical modification of chromatin can occur as a result of what two processes?
DNA methylation Histone acetylation
45
What is DNA methylation?
(Associated with gene silencing) - Attachment of methyl groups to DNA bases - Triggers formation of compact chromatin structure - Associated with inactive DNA - Accounts for genomic imprinting in mammals
46
What is histone acetylation?
(associated with gene activation) - Attachment of acetyl groups to histones - Acetylated histones grip DNA less tightly - Acetylation/deacetylation is involved in switching genes on/off
47
How changes in DNA methylation ​ and histone acetylation affect ​ chromatin structure?
Closed chromatin:​ DNA methylated; ​ histones not acetylated​ Open chromatin:​ DNA unmethylated; ​ histones acetylated
48
What are the three different RNA polymerases?
RNA polymerase I: ribosomal RNA RNA polymerase II: messenger RNA RNA polymerase III: small RNAs
49
Transcription begins when the RNA polymerase binds to a promoter, why?
DNA sequences adjacent to the gene (‘upstream’) that:​ - Determine where the transcription of the gene is initiated ​ - Determine the rate of transcription​ ​
50
Transcription begins when the RNA polymerase binds to a promoter. What is the TATA box?
A key part of the promoter ​ Provides the site of initial binding of the transcription initiation machinery​ Located 10-35 bp upstream of the transcription start site
51
Before transcription can start, ​ a preinitiation complex must form​, what is this? (step 1/2)
RNA polymerase can't bind to promoters on their own so uses aid by: 1.Binding of TFIID: includes the TATA-binding protein (TBP) + TATA-associated proteins (TAFs)​ 2. Sequential addition of other ‘general transcription factors’ – first TFIIA and TFIIB​ ​
52
Before transcription can start, ​ a preinitiation complex must form​, what is this? (step 3/4)
3. Then binding of TFIIF + ​RNA polymerase II​ 4. Followed by TFIIE +TFIIH- ​to form the preinitiation complex​
53
How are the rate of transcription​ is modulated in eukaryotes​?
The interaction between the transcription initiation complex and the basal promoter is very inefficient – so would produce very low level of gene expression​ The process is regulated by ‘specific transcription factors’ (‘activators’ or ‘repressors)​ These bind to ‘proximal control elements’ and ‘distal control elements’ (groupings of which are called ‘enhancers’)​
54
How do enhancers work when they may be 1000s of bps from the promoter?​
Folding of the DNA to bring distal sequences into proximity with the promoter
55
Modular structure of specific TFs
They have a separate DNA-binding and transcriptional activation domains (transcriptional domain is responsible for recruiting other proteins into the transcription factor complex)
56
What is Post-transcriptional regulation?
Processing of the primary transcript (in eukaryotes) - Capping of 5’ end​ - Polyadenylation of 3’ end​ - Splicing to remove introns​
57
What is alternative RNA splicing?
How one gene can code for >1 protein Regulatory proteins control intron-exon choices by binding to regulatory sequences within the primary transcript. Different mRNAs can be generated in different cell types
58
What does the alpha-tropomyosin gene specify?
Different forms of the protein in different muscle types
59
What can the Dscam gene generate?
>30,000 different proteins through alternative splicing.
60
Where are Dscam proteins located, what do they provide?
Dscam proteins are located on the surface of a growing neuron and provide a cell recognition mechanism that regulated brain development.
61
What is determination in the process of cell differentiation?
the process that leads up to the observable differentiation of a cell
62
By what process is cell differentiated state achieved?
Differentiated cells express different sets of genes​ - this is achieved by transcriptional regulation involving gene cascades
63
What is a gene cascade?
One main gene (Master regulatory gene) activated the expression of other genes which in turn causes activation of other genes until Cell-specific genes are activated
64
How does determination and differentiation occur from the precursor cell?
Signal transmitted to precursor cell, turning on Master regulatory gene (now a determined cell), which the master regulatory gene turns on cell-specific genes via a gene cascade which differentiates the cell
65
Determination and differentiation of muscle cells?
- Develop from embryonic precursor cells - Signals from other cells lead to activation of MyoD master regulatory gene encoding MyoD transcription factor - Cell determination occurred and cells = myoblasts - MyoD activates expression of other muscle-specific transcription factors - Causing activation of genes for muscle proteins and blocks cell division (non-dividing myoblasts fuse forming muscle fibres)
66
What did Eric Weischaus and Christianne Nusslein-Volhard screened for? To identify what?
Screened for Drosophila mutants that failed to develop beyond specific stages of embryogenesis​ to identify genes that determine Drosophila's body plan ('Pattern formation' genes)
67
What are the three main phases of Drosophila development?
1 - Establishing main axes, forming a synctial blastoderm 2 - Establishing segments (Head = 3, Thorax = 3, Abdomen = 9) 3 - Filling in the details, for example building various organs of animal (wings, legs, eyes, etc)
68
What is the Biocid mutant of drosophila?
Bicoid = "two-tailed" Abnormal larva from bicoid mutant mother (no anterior end, just two posterior ends)
69
What did Eric Weischaus and Christianne Nusslein-Volhard explain why Bicoid occurred in the drosophila?
- These determine polarity of egg and therefore fly, - Encode proteins/mRNAs enter the egg while it is still in ovary - So when maternal gene is defective, the eggs fail to develop normally (known as maternal effect genes) - Encode transcription factors, initiating a cascade of gene activations
70
A gradient of the Bicoid mRNA is already established in the unfertilized egg​ - how does this cause a bicoid drosophila?
Nurse cells pump bicoid mRNA into the egg cells into the unfertilised egg. At fertilization, the bicoid mRNA is translated into bicoid protein gradient in the early embryo which determines the anterior end of the fly.
71
What did Eric Weischaus and Christianne Nusslein-Volhard work establish?
The principle that a gradient of molecules can determine polarity and position of cells/proteins. (morphogens) Biocid and other morphogens are transcription factors which initiate a cascade of gene activations that regulate drosophila development
72
What are the three main classes of segmentation genes in drosophila?
Gap genes which induce pair-rule genes which induce segment polarity genes (which activates homeotic genes)
73
What do egg polarity genes determine and induce?
Determine anterior-posterior axis, inducing Gap genes which sub-divide the embryo into broad areas and induce Pair-rule genes, that establish pairs of segments which induces Segment polarity genes that establish anterior-posterior axis of each segment and induces homeotic genes
74
Mutations in gap genes in drosophila produce what?
A phenotype where part of the embrvo is missing
75
Edward Lewis found what mutants of drosophila?
Homeotic mutants (Finding the 3rd thoracic segment has been replaced by another copy of the 2nd thoracic segment, resulting in a second pair of wings he called this a Ultrabithorax mutant)
76
Why were Homeotic genes discovered?
- First identified as dominant mutations that changes identity of body parts
77
Homeotic genes in drosophila?
series of homeotic Hox gene determining identity of embryonic regions along the anterior-posterior axis ​ Hox genes encode transcription factors with a ​conserved DNA binding domain (the ‘homeobox’ domain)​ and they occur in clusters, arranged in the same order as the regions they affect (‘colinearity’)
78
How are Hox gene clusters conserved between flies and mammals?
Order of genes similar to flies and same order of expression along anterior-posterior axis Some mammalian Hox genes are so similar that they can be swapped
79
Hox genes link to evolutionary theories?
Hox genes may have played an important role in evolution - many differences in morphology between species/phyla appear to be due to evolutionary changes in Hox genes Hence why Hox gene clusters are conserved between flies and mammals

BIOL 113 - Genetics (4 decks)

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